X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.84 α = 70.35
b = 38.62 β = 83.05
c = 39.85 γ = 72.09
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-01-23
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915,0.97903,0.91162 SSRL BL9-2

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
1.6 29.62 96.7 -- 0.054 -- 3.3 -- 25860 -- -- --

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 1.6 29.618 -- 0.0 -- 25860 1291 96.46 -- 0.172 0.17 0.209 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 1.597 1.639 -- 77 1729 0.252 0.231 -- 91.58
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.754
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] -1.08
Anisotropic B[1][3] 1.11
Anisotropic B[2][2] 1.13
Anisotropic B[2][3] -1.16
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.645
r_mcbond_it 1.918
r_bond_refined_d 0.016
r_mcbond_other 0.527
r_scbond_it 5.39
r_scangle_it 8.55
r_chiral_restr 0.097
r_dihedral_angle_3_deg 13.339
r_angle_other_deg 1.151
r_dihedral_angle_1_deg 6.166
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 16.66
r_bond_other_d 0.002
r_mcangle_it 3.135
r_dihedral_angle_2_deg 36.175
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1837
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 217

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.5.0102
SCALA data scaling version: 3.3.15
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing