X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 292.0
Details 0.2 M MgCl2, 0.1 M sodium acetate pH 5.3 and 30% (v/v) MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.4 α = 90
b = 106.7 β = 109.2
c = 85.9 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-11-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.97242 APS 22-BM

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
1.9 30 99.6 0.056 -- -- 3.8 -- 80548 -- -3.0 26.9
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)
1.9 1.93 -- -- -- -- -- --

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 1.9 30.0 -- -- -- 79463 1069 99.86 -- 0.16154 0.16108 0.19594 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 1.9 1.949 -- 86 5794 0.24 0.371 -- 99.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.261
Anisotropic B[1][1] 1.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.81
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.06
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.988
r_mcbond_it 1.946
r_mcbond_other 1.945
r_long_range_B_refined 7.233
r_scbond_it 2.691
r_chiral_restr 0.098
r_dihedral_angle_2_deg 32.661
r_mcangle_other 2.873
r_long_range_B_other 7.103
r_scangle_other 4.228
r_bond_refined_d 0.014
r_gen_planes_other 0.002
r_dihedral_angle_1_deg 6.235
r_angle_refined_deg 1.583
r_dihedral_angle_4_deg 16.487
r_bond_other_d 0.002
r_gen_planes_refined 0.007
r_mcangle_it 2.874
r_scbond_other 2.691
r_dihedral_angle_3_deg 13.818
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5877
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 491

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-3000 data reduction
HKL-3000 data scaling
PHASER phasing