X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 2.0M magnesium chloride, 0.1M Sodium Iodide, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.29 α = 90
b = 81.55 β = 108.6
c = 128.53 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-20
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.918401, 0.979338 ALS 8.2.2

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
1.7 29.89 99.9 -- 0.106 -- 3.7 224161 224161 -- -- --
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)
1.7 1.74 99.8 0.959 0.959 0.7 3.7 16489

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 1.7 29.894 -- 0.0 -- 224086 11237 99.87 -- 0.1507 0.1492 0.1789 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 1.7 1.744 -- 814 15241 0.256 0.272 -- 99.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.5088
Anisotropic B[1][1] 0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.25
Anisotropic B[2][2] -0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.083
r_dihedral_angle_4_deg 15.127
r_dihedral_angle_3_deg 12.129
r_dihedral_angle_2_deg 33.591
r_dihedral_angle_1_deg 6.374
r_angle_other_deg 0.831
r_angle_refined_deg 1.299
r_bond_other_d 0.001
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13447
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 1973

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.6.0117 refinement
SCALA version: 3.3.20 phasing
SOLVE phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation