X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GNWPDB ENTRY 1GNW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.1α = 83.65
b = 113.72β = 79.47
c = 132.02γ = 65.85
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M2014-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
12.7787.5898.60.16.82.21269321.8
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)
12.772.8498.10.721.82.2

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 1GNW2.7787.58120813611698.590.252070.250420.28428RANDOM46.48
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]
0.89-1.70.3-2.01-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.549
r_dihedral_angle_4_deg23.255
r_dihedral_angle_3_deg19.477
r_dihedral_angle_1_deg5.801
r_mcangle_it4.768
r_scbond_it3.002
r_mcbond_it2.987
r_mcbond_other2.986
r_angle_other_deg2.472
r_angle_refined_deg1.913
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.549
r_dihedral_angle_4_deg23.255
r_dihedral_angle_3_deg19.477
r_dihedral_angle_1_deg5.801
r_mcangle_it4.768
r_scbond_it3.002
r_mcbond_it2.987
r_mcbond_other2.986
r_angle_other_deg2.472
r_angle_refined_deg1.913
r_chiral_restr0.11
r_bond_refined_d0.013
r_bond_other_d0.012
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms38370
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms336

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing