X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HID 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Internal tracking number 226144E11. JCSG screen condition E11: 14.4% PEG 8000 20% v/v glycerol 80 mM Cacodylate pH 6.5 160 mM Calcium acetate ButhA.00888.a.A1 PW33408 at 32.28 mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4750.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.88α = 109.35
b = 74.59β = 90.01
c = 112.66γ = 103.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.541780

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
11.955096.10.07914.145.1129329-323.361
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)
11.95290.80.44233.77

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 REPLACEMENTTHROUGHOUT3HID1.9550129328652796.170.2030.2010.247RANDOM19.263
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]
-1.060.860.362.380.59-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.704
r_dihedral_angle_4_deg16.049
r_dihedral_angle_3_deg13.775
r_dihedral_angle_1_deg6.644
r_angle_refined_deg1.441
r_angle_other_deg0.89
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.704
r_dihedral_angle_4_deg16.049
r_dihedral_angle_3_deg13.775
r_dihedral_angle_1_deg6.644
r_angle_refined_deg1.441
r_angle_other_deg0.89
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12667
Nucleic Acid Atoms
Solvent Atoms1128
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction