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_mcbond_it 1.501
r_scangle_it 5.356
r_dihedral_angle_1_deg 7.861
r_sphericity_bonded 2.598
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 36.708
r_dihedral_angle_4_deg 10.244
r_angle_other_deg 1.065
r_sphericity_free 11.076
r_dihedral_angle_3_deg 19.737
r_mcbond_other 0.437
r_chiral_restr 0.123
r_bond_other_d 0.001
r_rigid_bond_restr 2.01
r_angle_refined_deg 2.07
r_gen_planes_refined 0.01
r_bond_refined_d 0.025
r_mcangle_it 2.553
r_scbond_it 3.508
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

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
REFMAC refinement version: 5.5.0110
MOSFLM data reduction
SCALA data scaling