X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.630015% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.5351.45

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 mm2005-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.81EMBL/DESY, HAMBURGX13

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
11.91733.05999.7285781855403
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.96796.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1RJD1.9233.068578085540427699.720.2090.2060.268RANDOM16.465
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.109
r_dihedral_angle_4_deg16.75
r_dihedral_angle_3_deg16.125
r_dihedral_angle_1_deg6.504
r_scangle_it3.362
r_scbond_it2.292
r_angle_refined_deg1.875
r_mcangle_it1.37
r_mcbond_it0.936
r_symmetry_hbond_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.109
r_dihedral_angle_4_deg16.75
r_dihedral_angle_3_deg16.125
r_dihedral_angle_1_deg6.504
r_scangle_it3.362
r_scbond_it2.292
r_angle_refined_deg1.875
r_mcangle_it1.37
r_mcbond_it0.936
r_symmetry_hbond_refined0.319
r_nbtor_refined0.308
r_nbd_refined0.227
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.205
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7908
Nucleic Acid Atoms
Solvent Atoms624
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing