X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details PEG 8k, HEPES, MgOAc, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.05 α = 90
b = 88.05 β = 90
c = 117.59 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-03-06
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
3.1 15 94.2 0.187 0.187 -- 2.0 9867 9867 0.0 0.0 47.0
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)
3.1 3.21 94.0 0.397 0.397 2.6 2.0 964

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
FOURIER SYNTHESIS 3.1 15.0 0.0 0.0 8660 8660 447 92.3 0.284 0.28401 0.28295 0.30544 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 3.1 3.177 632 40 592 0.379 0.431 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model overall
Mean Isotropic B 2.352
Anisotropic B[1][1] -2.6
Anisotropic B[1][2] -1.3
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.9
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.624
r_scbond_it 0.446
r_mcangle_it 0.496
r_mcbond_it 0.36
r_symmetry_vdw_refined 0.179
r_xyhbond_nbd_refined 0.116
r_nbd_refined 0.198
r_gen_planes_refined 0.003
r_chiral_restr 0.059
r_dihedral_angle_1_deg 4.571
r_angle_refined_deg 0.954
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2362
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 0

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement