X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 16% PEG 6000, 10% Jeffamine M-600 (pH 7.0), 0.1M Tris-HCl (pH 8.0), 0.1M ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.67 α = 90
b = 36.67 β = 90
c = 144.39 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2008-10-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-5 0.9083 MAX II I911-5

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
2.2 20 93.2 0.059 -- -- 4.7 5811 5811 1.0 1.0 --
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)
2.2 2.3 82.7 0.49 -- 2.17 3.0 623

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 2.2 17.13 -- 0.0 -- 5250 559 93.47 -- 0.22914 0.22363 0.28087 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 2.2 2.256 -- 32 329 0.306 0.4 -- 82.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.17
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.624
r_bond_refined_d 0.015
r_angle_other_deg 1.743
r_mcbond_other 0.126
r_chiral_restr 0.089
r_dihedral_angle_1_deg 6.839
r_dihedral_angle_3_deg 18.798
r_mcangle_it 1.126
r_bond_other_d 0.001
r_scbond_it 1.698
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_angle_refined_deg 1.397
r_scangle_it 2.874
r_dihedral_angle_4_deg 21.184
r_dihedral_angle_2_deg 47.527
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 818
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 28

Software

Software
Software Name Purpose
MAR345 data collection
PHASER phasing
REFMAC refinement version: 5.5.0044
XDS data reduction
XDS data scaling