2V2M

Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2LPDB ENTRY 2V2L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18RESERVOIR: CADMIUM SULFATE 0.044M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.261.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.802α = 90
b = 182.802β = 90
c = 182.802γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHRH COATED, ZERODUR, VERTICAL FOCUSSING POSSIBLE2004-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.652599.70.0525.57.231920
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.71000.45.47.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2V2L1.65105.4130300161699.70.1870.1850.212RANDOM14.2
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.465
r_dihedral_angle_4_deg22.465
r_dihedral_angle_3_deg13.629
r_dihedral_angle_1_deg5.162
r_scangle_it4.599
r_scbond_it3.329
r_mcangle_it1.775
r_mcbond_it1.687
r_angle_refined_deg1.559
r_angle_other_deg0.953
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1363
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling