X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 0.2M Ca(OAc)2, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.17 α = 90
b = 102.52 β = 90
c = 51.51 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2007-07-20
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97944,0.97916 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
1.19 39.25 99.2 0.055 -- -- 3.6 -- 63440 -- -3.0 9.484
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)
1.19 1.22 98.0 0.525 0.525 2.5 3.6 --

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
MAD 1.19 39.253 -- 0.0 -- 63421 3215 99.05 -- 0.1358 0.1351 0.1504 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 1.19 1.221 -- 238 4381 0.22 0.251 -- 97.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.7661
Anisotropic B[1][1] 0.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.34
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 34.078
r_dihedral_angle_3_deg 12.545
r_bond_other_d 0.001
r_gen_planes_refined 0.01
r_mcbond_it 1.653
r_scbond_it 3.344
r_rigid_bond_restr 1.591
r_mcbond_other 0.82
r_dihedral_angle_4_deg 18.376
r_mcangle_it 2.471
r_sphericity_free 9.935
r_bond_refined_d 0.015
r_gen_planes_other 0.003
r_dihedral_angle_1_deg 6.394
r_sphericity_bonded 4.691
r_angle_other_deg 1.04
r_scangle_it 4.755
r_angle_refined_deg 1.833
r_chiral_restr 0.107
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1111
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 236

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: June 12
REFMAC refinement version: 5.5.0110
XDS data reduction
SHELXD phasing