X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RDH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Protein: 8.0 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3); Screen: PEGs (C10), 0.1M MES (pH 6.5), 25% (w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.427α = 90
b = 90.623β = 90
c = 159.711γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2014-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.93095.40.1210.12110.44.21366813668-358.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.951000.50.52.74.3714

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 REPLACEMENTTHROUGHOUT2RDH2.929.961225312253137295.010.231430.231430.225620.28252RANDOM54.042
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]
-3.76-1.675.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.031
r_dihedral_angle_4_deg12.522
r_dihedral_angle_3_deg11.672
r_long_range_B_refined6.897
r_long_range_B_other6.875
r_mcangle_it4.152
r_mcangle_other4.152
r_scangle_other4.123
r_mcbond_it2.52
r_mcbond_other2.519
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.031
r_dihedral_angle_4_deg12.522
r_dihedral_angle_3_deg11.672
r_long_range_B_refined6.897
r_long_range_B_other6.875
r_mcangle_it4.152
r_mcangle_other4.152
r_scangle_other4.123
r_mcbond_it2.52
r_mcbond_other2.519
r_scbond_it2.445
r_scbond_other2.418
r_dihedral_angle_1_deg2.078
r_angle_refined_deg1.538
r_angle_other_deg1.03
r_chiral_restr0.09
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4588
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms3

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling