X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.75
Temperature 293.0
Details 0.2M magnesium chloride, 24.0% polyethylene glycol 400, 0.1M HEPES pH 6.75, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.87 α = 90
b = 85.6 β = 90
c = 149.09 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2013-12-13
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 0.97939,0.96109,0.97919 SSRL BL14-1

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
2 29.35 97.8 0.05 -- -- -- -- 27920 -- -3.0 35.548
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)
2.0 2.07 92.5 0.609 -- 1.4 -- --

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 2.0 29.355 -- 0.0 -- 27918 1403 99.48 -- 0.1705 0.1682 0.2159 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 2.0 2.052 -- 84 1911 0.311 0.297 -- 98.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.1123
Anisotropic B[1][1] -2.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.19
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 38.588
r_mcbond_it 2.735
r_bond_refined_d 0.019
r_dihedral_angle_3_deg 15.107
r_dihedral_angle_4_deg 17.122
r_chiral_restr 0.097
r_mcangle_it 4.009
r_dihedral_angle_1_deg 6.394
r_angle_other_deg 0.824
r_angle_refined_deg 1.779
r_gen_planes_other 0.001
r_mcbond_other 2.736
r_bond_other_d 0.001
r_gen_planes_refined 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2693
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 193

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling
REFMAC refinement version: 5.8.0049
XDS data reduction
SHELXD phasing