X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NMW3NMW, 2PZ1
experimental modelPDB 2PZ13NMW, 2PZ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62771M lithium sulfate, 0.5M ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.974.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.175α = 90
b = 163.175β = 90
c = 242.593γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2010-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A

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
135096.10.05715.15.646293
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)
133.1169.20.4064.33347

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 REPLACEMENTTHROUGHOUT3NMW, 2PZ13.015043230220290.240.25050.24870.2839RANDOM82.824
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_3_deg17.616
r_dihedral_angle_4_deg16.088
r_dihedral_angle_1_deg4.1
r_angle_refined_deg0.861
r_scangle_it0.416
r_scbond_it0.24
r_mcangle_it0.144
r_mcbond_it0.072
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.634
r_dihedral_angle_3_deg17.616
r_dihedral_angle_4_deg16.088
r_dihedral_angle_1_deg4.1
r_angle_refined_deg0.861
r_scangle_it0.416
r_scbond_it0.24
r_mcangle_it0.144
r_mcbond_it0.072
r_chiral_restr0.057
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7546
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction