2V2S

Mutant R59M recombinant horse spleen apoferritin crystallized in acidic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2NPDB ENTRY 2V2N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 1.1M, SODIUM ACETATE 0.1M PH5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.242α = 90
b = 181.242β = 90
c = 181.242γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR 2 BENT, VERTICALLY FOCUSSING2007-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.372399.90.11510.953821
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)
11.371.598.80.564.210.2

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 2V2N1.37104.8351086273599.90.2030.2020.226RANDOM13.32
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_deg37.722
r_dihedral_angle_4_deg21.343
r_dihedral_angle_3_deg13.018
r_dihedral_angle_1_deg5.015
r_scangle_it4.964
r_scbond_it3.581
r_mcangle_it1.816
r_mcbond_it1.746
r_angle_refined_deg1.708
r_angle_other_deg1.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.722
r_dihedral_angle_4_deg21.343
r_dihedral_angle_3_deg13.018
r_dihedral_angle_1_deg5.015
r_scangle_it4.964
r_scbond_it3.581
r_mcangle_it1.816
r_mcbond_it1.746
r_angle_refined_deg1.708
r_angle_other_deg1.097
r_symmetry_vdw_refined0.38
r_symmetry_vdw_other0.28
r_nbd_refined0.261
r_xyhbond_nbd_refined0.204
r_nbd_other0.203
r_symmetry_hbond_refined0.199
r_nbtor_refined0.182
r_chiral_restr0.128
r_nbtor_other0.088
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms1366
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling