X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R7KPDB entry 2R7K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.129130% MPD, 100 mM Na/K phosphate, pH 6.1, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
5.2876.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.477α = 90
b = 122.477β = 90
c = 560.925γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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
12.55097.90.05711.67.55598455970
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)
2.52.5981.90.2836.14588

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 REPLACEMENTTHROUGHOUTPDB entry 2R7K2.539.975598455970287497.840.2190.2190.2180.239RANDOM47.904
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]
1.860.931.86-2.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_3_deg14.795
r_dihedral_angle_4_deg11.642
r_dihedral_angle_1_deg5.628
r_scangle_it1.676
r_angle_refined_deg1.024
r_scbond_it0.94
r_mcangle_it0.87
r_mcbond_it0.463
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_3_deg14.795
r_dihedral_angle_4_deg11.642
r_dihedral_angle_1_deg5.628
r_scangle_it1.676
r_angle_refined_deg1.024
r_scbond_it0.94
r_mcangle_it0.87
r_mcbond_it0.463
r_nbtor_refined0.305
r_nbd_refined0.18
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.103
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5302
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling