X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.08M sodium cacodylate pH 6.5, 20% glycerol, 16% polyethylene glycol 8000, 0.16M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 148.65 α = 90
b = 84.14 β = 98.31
c = 53.03 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 double crystal monochromator 2012-05-03
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97922 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
2.55 45.97 99.8 0.076 -- -- -- -- 21164 -- -3.0 62.923
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)
2.55 2.64 100.0 0.739 -- 2.1 -- --

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 2.55 45.971 -- 0.0 -- 21159 1088 99.72 -- 0.1899 0.1883 0.218 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 2.55 2.616 -- 79 1421 0.333 0.353 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.0088
Anisotropic B[1][1] 3.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.53
Anisotropic B[2][2] -4.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.93
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.004
r_gen_planes_refined 0.006
r_chiral_restr 0.098
r_dihedral_angle_4_deg 19.905
r_dihedral_angle_3_deg 11.245
r_dihedral_angle_2_deg 34.916
r_dihedral_angle_1_deg 3.608
r_angle_other_deg 1.404
r_angle_refined_deg 1.646
r_bond_other_d 0.004
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3893
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 26

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.6.0117 refinement
Xscale version: December 29, 2011 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation