X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ML4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289pACT E10: 0.2 M sodium monobasic phosphate/potassium dibasic phosphate, 20% PEG 3350, protein at 18.47 mg/ml K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.98α = 90
b = 134.55β = 90
c = 159.46γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2012-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.15097.10.1278.93105706102675-3
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)
12.12.1591.80.5552.61

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 REPLACEMENTTHROUGHOUT1ML42.149.4810570697768513497.170.193810.191460.23807RANDOM25.475
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]
-1.16-0.231.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_4_deg18.857
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg6.219
r_angle_refined_deg1.506
r_mcangle_it1.004
r_angle_other_deg0.808
r_scbond_it0.682
r_mcbond_it0.601
r_mcbond_other0.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.214
r_dihedral_angle_4_deg18.857
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg6.219
r_angle_refined_deg1.506
r_mcangle_it1.004
r_angle_other_deg0.808
r_scbond_it0.682
r_mcbond_it0.601
r_mcbond_other0.601
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13462
Nucleic Acid Atoms
Solvent Atoms868
Heterogen Atoms45

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing