X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.7
Temperature 298.0
Details 0.07M tris, 0.2 M magnesium chloride, 16% PEG 4000, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.65 α = 90
b = 78.34 β = 90
c = 119.43 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2009-06-04
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.5 39.16 98.8 0.058 -- -- 4.8 8009 7913 3.0 2.0 --
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)
2.5 2.64 98.4 0.363 -- 4.1 4.9 --

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 2.5 30.55 -- -- -- 7527 382 98.02 -- 0.19021 0.18706 0.25257 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 2.5 2.565 -- 34 534 0.279 0.459 -- 97.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.523
Anisotropic B[1][1] 0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.598
r_sphericity_free 11.076
r_rigid_bond_restr 2.01
r_scangle_it 5.356
r_scbond_it 3.508
r_mcangle_it 2.553
r_mcbond_other 0.437
r_mcbond_it 1.501
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_chiral_restr 0.123
r_dihedral_angle_4_deg 10.244
r_dihedral_angle_3_deg 19.737
r_dihedral_angle_2_deg 36.708
r_dihedral_angle_1_deg 7.861
r_angle_other_deg 1.065
r_angle_refined_deg 2.07
r_bond_other_d 0.001
r_bond_refined_d 0.025
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1726
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 60

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER model building
CrystalClear data collection