X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 277.0
Details NANODROP, 0.2M NH4OAc, 30.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.14 α = 90
b = 42.38 β = 103.87
c = 154.01 γ = 90
Symmetry
Space Group C 1 2 1

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) 2007-11-20
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 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
1.85 40.83 99.5 0.146 0.146 -- 5.2 -- 45283 -- -- 13.78
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)
1.85 1.95 97.2 0.611 0.611 1.3 4.6 6400

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 1.85 40.825 -- 0.0 -- 45282 2285 99.41 -- 0.188 0.185 0.242 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 1.85 1.898 -- 165 2985 0.294 0.339 -- 94.48
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.309
Anisotropic B[1][1] 0.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.0
Anisotropic B[2][2] 0.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.33
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_scangle_it 3.457
r_scbond_it 2.338
r_dihedral_angle_2_deg 43.209
r_dihedral_angle_1_deg 5.831
r_mcbond_other 0.213
r_mcangle_it 1.369
r_angle_other_deg 1.011
r_angle_refined_deg 1.488
r_chiral_restr 0.089
r_bond_refined_d 0.016
r_dihedral_angle_3_deg 14.089
r_gen_planes_refined 0.007
r_dihedral_angle_4_deg 16.748
r_mcbond_it 0.797
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4152
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 492

Software

Software
Software Name Purpose
REFMAC refinement version: 5.4.0062
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling
PDB_EXTRACT data extraction version: 3.000
MAR345 data collection version: CCD
XDS data reduction
SHARP phasing
SHELXD phasing