X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RJDPDB ENTRY 1RJD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.630015% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.652.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.62α = 90
b = 110.62β = 90
c = 161.94γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSi(111) Mirror2005-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.81EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.983.04599.97880898806033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9595.6

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 1RJD1.983.0488060440499.970.1840.1820.224RANDOM22.207
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]
0.630.320.63-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg14.313
r_dihedral_angle_1_deg5.55
r_scangle_it3.871
r_scbond_it2.534
r_mcangle_it1.619
r_angle_refined_deg1.524
r_mcbond_it1.009
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_dihedral_angle_4_deg16.85
r_dihedral_angle_3_deg14.313
r_dihedral_angle_1_deg5.55
r_scangle_it3.871
r_scbond_it2.534
r_mcangle_it1.619
r_angle_refined_deg1.524
r_mcbond_it1.009
r_nbtor_refined0.311
r_symmetry_hbond_refined0.259
r_symmetry_vdw_refined0.255
r_nbd_refined0.223
r_xyhbond_nbd_refined0.193
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7853
Nucleic Acid Atoms
Solvent Atoms913
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing