X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JI3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277NaCl, Na succinate, DMSO, isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5150.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.31α = 90
b = 77.96β = 90
c = 169.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMARRESEARCH1994-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X311.0EMBL/DESY, HAMBURGX31

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.8626.71990.0886.12292922929
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.862.9399.71663

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JI32.8626.71229292292923221000.2130.2130.2080.263RANDOM18.51
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]
0.04-0.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_3_deg19.114
r_dihedral_angle_4_deg18.157
r_dihedral_angle_1_deg4.783
r_angle_refined_deg0.786
r_angle_other_deg0.584
r_scangle_it0.582
r_scbond_it0.355
r_mcangle_it0.286
r_symmetry_vdw_other0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.146
r_dihedral_angle_3_deg19.114
r_dihedral_angle_4_deg18.157
r_dihedral_angle_1_deg4.783
r_angle_refined_deg0.786
r_angle_other_deg0.584
r_scangle_it0.582
r_scbond_it0.355
r_mcangle_it0.286
r_symmetry_vdw_other0.231
r_xyhbond_nbd_refined0.216
r_nbd_refined0.202
r_nbd_other0.192
r_nbtor_refined0.19
r_symmetry_vdw_refined0.172
r_mcbond_it0.164
r_metal_ion_refined0.13
r_symmetry_hbond_refined0.126
r_nbtor_other0.088
r_chiral_restr0.049
r_mcbond_other0.03
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6143
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms4

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling