X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 40% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.86 α = 90
b = 59.47 β = 97.94
c = 34.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD multi-layer optics 2012-12-04
Diffraction Radiation
Monochromator Protocol
Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE MICROSOURCE 1.54 -- --

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
1.6 50 99.8 0.021 -- -- 10.13 16317 16317 0.0 0.0 20.4
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)
1.6 1.63 95.3 0.2199 -- 4.49 2.55 572

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 1.6 34.13 -- 0.0 16297 16297 825 99.77 0.1518 0.1518 0.1503 0.1789 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 1.6 1.642 -- 65 1121 0.166 0.203 -- 97.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.7204
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.11
Anisotropic B[2][2] 0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.48
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.004
r_gen_planes_refined 0.012
r_chiral_restr 0.107
r_dihedral_angle_4_deg 10.562
r_dihedral_angle_3_deg 13.903
r_dihedral_angle_2_deg 36.264
r_dihedral_angle_1_deg 6.043
r_angle_other_deg 0.886
r_angle_refined_deg 1.942
r_bond_other_d 0.001
r_bond_refined_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1083
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 138

Software

Computing
Computing Package Purpose
APEX Data Collection
SAINT Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement
SAINT data reduction