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_bond_refined_d 0.012
r_angle_other_deg 1.404
r_gen_planes_refined 0.006
r_angle_refined_deg 1.646
r_dihedral_angle_4_deg 19.905
r_chiral_restr 0.098
r_gen_planes_other 0.004
r_dihedral_angle_1_deg 3.608
r_dihedral_angle_3_deg 11.245
r_dihedral_angle_2_deg 34.916
r_bond_other_d 0.004
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

Software
Software Name Purpose
MOLPROBITY validation version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: December 29, 2011
REFMAC refinement version: 5.6.0117
XDS data reduction
SHELXD phasing