X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.4
Temperature 298.0
Details 10.5% PEG 400, 0.05 M Tris-Cl pH 8.4, 0.3 M NaCl, 0.01 M DTT, 0.01M EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.88 α = 90
b = 97.88 β = 90
c = 80.62 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.3 29.8 80.9 -- -- -- -- 21340 17271 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)
-- -- -- -- -- -- -- --

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 2.3 29.77 -- 0.0 15715 15715 1769 89.25 -- 0.21484 0.21125 0.24564 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 2.3 2.359 -- 157 1245 0.334 0.386 -- 97.63
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.024
Anisotropic B[1][1] 0.9
Anisotropic B[1][2] 0.45
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.35
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.687
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_chiral_restr 0.094
r_dihedral_angle_3_deg 16.202
r_scangle_it 3.128
r_scbond_it 2.02
r_angle_other_deg 0.96
r_dihedral_angle_2_deg 35.61
r_mcangle_it 1.251
r_bond_refined_d 0.016
r_dihedral_angle_1_deg 6.856
r_mcbond_other 0.15
r_gen_planes_refined 0.006
r_dihedral_angle_4_deg 20.728
r_angle_refined_deg 1.705
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2230
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 124

Software

Software
Software Name Purpose
CrystalClear data collection
AMoRE phasing
REFMAC refinement version: 5.4.0078
d*TREK data reduction
d*TREK data scaling