X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 297.0
Details 25% PEG3350, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78 α = 90
b = 78 β = 90
c = 101.61 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2005-09-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E 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
1.85 42.6 99.8 -- 0.063 -- 8.4 27404 27404 0.0 0.0 --
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)
1.85 1.9 99.3 -- 0.469 3.3 6.3 2662

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
SAD 1.85 42.6 -- 0.0 25999 25999 1378 99.82 0.19766 0.19766 0.1958 0.23334 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 1.85 1.898 -- 101 1866 0.251 0.347 -- 99.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.118
Anisotropic B[1][1] -0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.36
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.298
r_scbond_it 2.684
r_mcangle_it 1.977
r_mcbond_it 1.139
r_symmetry_hbond_refined 0.25
r_symmetry_vdw_refined 0.236
r_bond_refined_d 0.017
r_angle_refined_deg 1.728
r_dihedral_angle_1_deg 4.379
r_dihedral_angle_2_deg 36.715
r_dihedral_angle_3_deg 13.011
r_dihedral_angle_4_deg 13.097
r_chiral_restr 0.112
r_gen_planes_refined 0.007
r_nbd_refined 0.23
r_nbtor_refined 0.312
r_xyhbond_nbd_refined 0.201
r_metal_ion_refined 0.128
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1876
Nucleic Acid Atoms 0
Heterogen Atoms 134
Solvent Atoms 236

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
BNP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement