X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 291.0
Details 20% PEG 3350, 0.2 M ammonium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Method Vapor Diffusion
Temperature 291.0
Details 20% PEG 3350, 0.2 M ammonium nitrate, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 150.06 α = 90
b = 65.57 β = 90
c = 28.76 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-09-14
CCD RAYONIX MX-300 -- 2012-09-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
1.72 75.03 100.0 -- 0.072 -- 7.1 31276 31276 -- -- --
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)
1.72 1.81 100.0 0.961 0.961 0.8 7.3 4483

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
MOLECULAR REPLACEMENT 1.72 37.54 -- 0.0 -- 31215 1583 99.98 -- 0.1781 0.1765 0.2072 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 1.72 1.765 -- 114 2145 0.29 0.299 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.6186
Anisotropic B[1][1] -1.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.56
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.094
r_dihedral_angle_4_deg 17.291
r_dihedral_angle_3_deg 12.65
r_dihedral_angle_2_deg 34.199
r_dihedral_angle_1_deg 4.854
r_angle_other_deg 0.824
r_angle_refined_deg 1.524
r_bond_other_d 0.001
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1849
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 168

Software

Computing
Computing Package Purpose
xds Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
shelx(siras), phaser Structure Solution
REFMAC 5.7.0027 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0027 refinement
SHELX phasing
SCALA version: 3.3.20 data reduction