2V2I

Wild type recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HRSPDB ENTRY 1HRS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5RESERVOIR: CADMIUM SULFATE 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M DROP 2 UL PROTEIN AND 2UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.261

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.334α = 90
b = 182.334β = 90
c = 182.334γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHTWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.2003-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
122099.70.0632.19.818049
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)
122.0596.40.346.25.5

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 1HRS2201686991998.30.1790.1770.217RANDOM19.91
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_deg37.517
r_dihedral_angle_4_deg21.614
r_dihedral_angle_3_deg14.728
r_scangle_it9.168
r_dihedral_angle_1_deg6.641
r_scbond_it6.244
r_mcbond_it3.644
r_mcangle_it3.531
r_angle_refined_deg1.457
r_angle_other_deg0.951
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.517
r_dihedral_angle_4_deg21.614
r_dihedral_angle_3_deg14.728
r_scangle_it9.168
r_dihedral_angle_1_deg6.641
r_scbond_it6.244
r_mcbond_it3.644
r_mcangle_it3.531
r_angle_refined_deg1.457
r_angle_other_deg0.951
r_symmetry_vdw_refined0.334
r_nbd_refined0.258
r_symmetry_vdw_other0.226
r_xyhbond_nbd_refined0.224
r_nbd_other0.213
r_symmetry_hbond_refined0.207
r_nbtor_refined0.19
r_chiral_restr0.113
r_nbtor_other0.094
r_gen_planes_refined0.023
r_bond_refined_d0.018
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms1363
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling