4KOD

Structure of p97 N-D1 R155H mutant in complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82880.1M citrate, pH 5.8, 0.3M NaCl, 13.6% EPG 3350, 20% glycerol, 0.625% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.52α = 90
b = 170.737β = 90
c = 256.601γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6921.9988.1118808-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.0651.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.9621.99112289593788.010.269560.268410.29094RANDOM120.557
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
3.67-9.125.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_3_deg18.914
r_dihedral_angle_4_deg16.422
r_dihedral_angle_1_deg6.182
r_scangle_it1.768
r_angle_refined_deg1.256
r_mcangle_it0.978
r_scbond_it0.948
r_angle_other_deg0.807
r_mcbond_it0.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_3_deg18.914
r_dihedral_angle_4_deg16.422
r_dihedral_angle_1_deg6.182
r_scangle_it1.768
r_angle_refined_deg1.256
r_mcangle_it0.978
r_scbond_it0.948
r_angle_other_deg0.807
r_mcbond_it0.525
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41268
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms324

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling