X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 293.0
Details 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6.2 - 6.5, 1.0 - 1.6 M ammonium sulphate and 0 - 10 % dioxane.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 125.53 α = 90
b = 125.53 β = 90
c = 200.91 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 180 mm plate -- 1998-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.5 0.87 SRS PX9.5

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
2.8 54.2 96.0 0.071 -- -- 5.9 18652 18652 0.0 0.0 36.1
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)
2.8 3.0 76.7 0.257 -- 2.9 3.7 --

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 2.83 44.38 -- -- -- 17779 872 95.61 -- 0.1687 0.1653 0.23785 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 2.833 2.906 -- 5 795 0.272 0.72 -- 56.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.13
Anisotropic B[1][1] -1.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.08
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.655
r_scbond_other 4.588
r_dihedral_angle_2_deg 37.961
r_scangle_other 7.182
r_dihedral_angle_4_deg 17.986
r_scbond_it 4.587
r_mcbond_it 4.163
r_mcbond_other 4.159
r_long_range_B_refined 11.049
r_gen_planes_other 0.002
r_chiral_restr 0.085
r_mcangle_it 6.674
r_mcangle_other 6.674
r_long_range_B_other 11.032
r_angle_other_deg 1.224
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 6.253
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 18.071
r_bond_other_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4825
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 120

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0107
MOSFLM data reduction
SCALA data scaling