X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 3% dioxane, 100mM MES, 1.5M (NH4)2SO4, pH 6.0, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.42 α = 90
b = 83.42 β = 90
c = 153.37 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX315HE -- 2012-01-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U

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
2.2 76.7 99.1 0.072 -- -- 5.5 30376 n/a -- -- 43.4
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)
2.2 2.28 99.4 -- -- -- -- --

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 2.2 76.7 -- 0.0 30376 30343 1557 98.97 -- 0.1981 0.1954 0.2484 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 2.199 2.256 -- 114 2107 0.229 0.303 -- 98.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.5095
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 39.091
r_dihedral_angle_4_deg 19.705
r_angle_refined_deg 1.588
MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 2.894
SIDE-CHAIN BOND REFINED ATOMS (A''2) 3.699
r_dihedral_angle_1_deg 5.67
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 17.019
r_bond_refined_d 0.015
SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 5.994
CHIRAL-CENTER RESTRAINTS (A''3) 0.131
MAIN-CHAIN BOND REFINED ATOMS (A''2) 1.632
RIGID-BOND RESTRAINTS (A''2) 2.036
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4183
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 135

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing