5FJD

APO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORIUM OB3B


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AJFPDB ENTRY 5AJF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M BIS-TRIS, PH 6.5, 25% W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9336

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.885α = 90
b = 105.918β = 112.52
c = 48.657γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.544.9599.70.0710.93.7608962
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)
11.51.5399.80.52.63.7

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 5AJF1.552.9657772308999.670.125350.122490.17913RANDOM17.052
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]
-0.20.99-0.6-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.101
r_dihedral_angle_2_deg29.122
r_dihedral_angle_4_deg20.673
r_sphericity_bonded13.963
r_dihedral_angle_3_deg13.118
r_rigid_bond_restr5.34
r_scbond_it4.118
r_dihedral_angle_1_deg4.034
r_mcangle_it2.427
r_angle_other_deg2.126
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.101
r_dihedral_angle_2_deg29.122
r_dihedral_angle_4_deg20.673
r_sphericity_bonded13.963
r_dihedral_angle_3_deg13.118
r_rigid_bond_restr5.34
r_scbond_it4.118
r_dihedral_angle_1_deg4.034
r_mcangle_it2.427
r_angle_other_deg2.126
r_mcbond_it2.116
r_mcbond_other2.111
r_angle_refined_deg1.786
r_chiral_restr0.107
r_bond_refined_d0.02
r_bond_other_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.011
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3140
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing