X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2IPDB ENTRY 2V2I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE BUFFER 0.1M PH 5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182α = 90
b = 182β = 90
c = 182γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSECOND CRYSTAL SAGITALLY BENT2008-06-20MSINGLE 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
11.52298.90.0432.211.17723826.6
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)
11.51.7598.60.554.610.8

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 2V2I1.5104.8339300208499.20.2050.2040.236RANDOM22.18
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_deg35.983
r_dihedral_angle_4_deg14.679
r_dihedral_angle_3_deg13.577
r_dihedral_angle_1_deg4.956
r_scangle_it4.929
r_scbond_it3.064
r_mcangle_it1.963
r_angle_refined_deg1.556
r_mcbond_it1.224
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.983
r_dihedral_angle_4_deg14.679
r_dihedral_angle_3_deg13.577
r_dihedral_angle_1_deg4.956
r_scangle_it4.929
r_scbond_it3.064
r_mcangle_it1.963
r_angle_refined_deg1.556
r_mcbond_it1.224
r_nbtor_refined0.309
r_nbd_refined0.232
r_symmetry_hbond_refined0.232
r_symmetry_vdw_refined0.197
r_xyhbond_nbd_refined0.152
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1364
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling