X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 303.0
Details 50 mM HEPES pH 7, 0.1 M KCl, 0.01 M MgCl2, and 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 161.63 α = 90
b = 161.63 β = 90
c = 58.23 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-06-21
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.91 29.1 99.5 0.069 0.076 -- 6.2 -- 19283 0.0 0.0 35.4
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)
2.91 3.04 96.5 0.566 0.519 3.4 6.3 2264

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 2.91 29.1 -- 0.0 19283 18292 989 99.55 0.20473 0.20473 0.20141 0.267 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 2.91 2.984 1263 58 1263 0.287 0.399 -- 94.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.398
Anisotropic B[1][1] -2.21
Anisotropic B[1][2] -1.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.32
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.434
r_mcbond_other 0.039
r_scbond_it 1.086
r_mcbond_it 0.282
r_angle_refined_deg 1.035
r_dihedral_angle_3_deg 16.226
r_dihedral_angle_2_deg 32.614
r_bond_other_d 0.001
r_scangle_it 1.584
r_angle_other_deg 0.817
r_dihedral_angle_4_deg 16.247
r_chiral_restr 0.056
r_mcangle_it 0.555
r_bond_refined_d 0.008
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4940
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 4

Software

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
REFMAC refinement version: 5.5.0109
XDS data reduction
SCALA data scaling