X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 0.1M HEPES pH 7.5, 40% polyethylene glycol 400, 0.2M calcium acetate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.75 α = 90
b = 55.49 β = 90
c = 76.18 γ = 90
Symmetry
Space Group P 21 21 21

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 2015-02-12
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 0.95369,0.97946,0.9793 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
1 29.3 98.2 0.038 -- -- 2.035 -- 72996 -- -3.0 6.458
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)
1.0 1.04 93.4 0.644 -- 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 1.0 29.304 -- 0.0 -- 72915 3681 99.41 -- 0.117 0.116 0.1365 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 1.0 1.027 -- 240 4913 0.274 0.245 -- 96.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.2306
Anisotropic B[1][1] -0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_angle_other_deg 1.01
r_gen_planes_refined 0.008
r_mcbond_it 0.684
r_sphericity_bonded 7.062
r_mcbond_other 0.676
r_dihedral_angle_2_deg 36.31
r_angle_refined_deg 1.721
r_gen_planes_other 0.002
r_mcangle_it 0.892
r_dihedral_angle_3_deg 10.315
r_dihedral_angle_1_deg 6.208
r_dihedral_angle_4_deg 10.384
r_sphericity_free 25.909
r_chiral_restr 0.115
r_rigid_bond_restr 2.399
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1114
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 232

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: November 3, 2014 BUILT=20141118
REFMAC refinement version: 5.8.0107
SHELXD phasing
XDS data reduction