X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 277.0
Details 40.00% polyethylene glycol 600, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.63 α = 90
b = 103.23 β = 90
c = 43.23 γ = 90
Symmetry
Space Group C 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-01-23
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.4 27.89 96.7 0.023 -- -- -- -- 21177 -- -3.0 17.296
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.4 1.45 95.8 0.393 -- 2.3 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.4 27.894 -- 0.0 -- 21177 1086 98.88 -- 0.1832 0.1819 0.2085 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4 1.437 -- 69 1439 0.279 0.263 -- 98.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.812
Anisotropic B[1][1] -1.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.79
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.822
r_bond_other_d 0.002
r_angle_refined_deg 1.126
r_mcangle_it 1.356
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 4.987
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 11.447
r_gen_planes_refined 0.007
r_chiral_restr 0.088
r_dihedral_angle_2_deg 34.839
r_dihedral_angle_4_deg 12.599
r_angle_other_deg 0.65
r_mcbond_it 0.936
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 854
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 115

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: July 4, 2012
REFMAC refinement version: 5.7.0032
XDS data reduction
SHELXD phasing