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_angle_other_deg 0.886
r_dihedral_angle_1_deg 6.043
r_bond_other_d 0.001
r_angle_refined_deg 1.942
r_dihedral_angle_3_deg 13.903
r_chiral_restr 0.107
r_bond_refined_d 0.018
r_dihedral_angle_4_deg 10.562
r_gen_planes_refined 0.012
r_gen_planes_other 0.004
r_dihedral_angle_2_deg 36.264
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

Software
Software Name Purpose
SAINT data reduction
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
APEX data collection
SAINT data scaling