X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 297.0
Details 0.2M sodium formate, 20% PEG3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.32 α = 90
b = 86.44 β = 101.26
c = 77.4 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 0
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 4r -- 2012-07-13
Diffraction Radiation
Monochromator Protocol
Graphite MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9218 DIAMOND I04

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
3.06 33.92 99.4 0.093 0.09 -- 7.5 18405 18304 2.4 2.0 35.0
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)
3.06 3.16 93.8 0.773 0.76 2.6 6.9 1260

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 3.08 29.71 -- -- 18405 17787 960 99.85 -- 0.32283 0.32051 0.36425 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 3.08 3.139 -- 69 1234 0.323 0.306 -- 99.69
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 100.413
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.03
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.47
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_chiral_restr 0.11
r_dihedral_angle_4_deg 18.623
r_dihedral_angle_3_deg 21.188
r_dihedral_angle_2_deg 37.494
r_dihedral_angle_1_deg 6.856
r_angle_refined_deg 1.531
r_bond_refined_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.025
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 4.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.36
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6838
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
EDNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXS Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
SHELXS model building
EDNA data collection