X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 5.0000% PEG-1000, 40.0000% PEG-300, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.23 α = 90
b = 79.23 β = 90
c = 144.59 γ = 120
Symmetry
Space Group P 31 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) 2008-11-12
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97870,0.97821 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
1.75 26.7 99.6 0.051 -- -- -- -- 53599 -- -3.0 24.896
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)
1.75 1.81 97.5 0.578 -- 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
MAD 1.75 26.698 -- 0.0 -- 53552 2716 99.66 -- 0.144 0.143 0.162 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 1.75 1.795 -- 206 3639 0.184 0.226 -- 97.47
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.319
Anisotropic B[1][1] -0.93
Anisotropic B[1][2] -0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.39
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.477
r_angle_other_deg 1.431
r_scbond_it 4.233
r_angle_refined_deg 1.675
r_dihedral_angle_2_deg 32.47
r_mcbond_it 1.445
r_bond_other_d 0.002
r_chiral_restr 0.102
r_bond_refined_d 0.015
r_dihedral_angle_1_deg 4.206
r_gen_planes_refined 0.008
r_gen_planes_other 0.003
r_scangle_it 6.539
r_dihedral_angle_4_deg 20.981
r_mcangle_it 2.227
r_dihedral_angle_3_deg 10.424
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2843
Nucleic Acid Atoms 0
Heterogen Atoms 123
Solvent Atoms 390

Software

Software
Software Name Purpose
REFMAC refinement version: 5.4.0067
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing