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_scangle_it 1.584
r_scbond_it 1.086
r_mcangle_it 0.555
r_mcbond_other 0.039
r_bond_refined_d 0.008
r_bond_other_d 0.001
r_angle_refined_deg 1.035
r_angle_other_deg 0.817
r_dihedral_angle_1_deg 5.434
r_dihedral_angle_2_deg 32.614
r_dihedral_angle_3_deg 16.226
r_dihedral_angle_4_deg 16.247
r_chiral_restr 0.056
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_mcbond_it 0.282
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
Phaser model building
MAR345dtb data collection