X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 289.0
Details 0.1 M sodium acetate trihydrate pH 4.6, 1 M magnesium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.09 α = 90
b = 65.16 β = 124.95
c = 86.39 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2012-06-07
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID

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
2.55 50 99.4 -- 0.057 -- 3.6 20436 20436 0.0 0.0 72.1
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)
2.55 2.59 98.6 -- 0.677 2.1 3.0 1006

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 2.551 33.747 -- 0.0 20378 20378 1046 98.54 0.188 0.188 0.185 0.241 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 2.5512 2.6856 2755 134 2621 0.2711 0.3396 -- 95.0
X Ray Diffraction 2.6856 2.8538 2948 151 2797 0.2436 0.3276 -- 100.0
X Ray Diffraction 2.8538 3.074 2931 140 2791 0.2379 0.2849 -- 100.0
X Ray Diffraction 3.074 3.3831 2922 134 2788 0.2059 0.2838 -- 100.0
X Ray Diffraction 3.3831 3.872 2944 152 2792 0.1948 0.2673 -- 100.0
X Ray Diffraction 3.872 4.876 2947 164 2783 0.1569 0.2333 -- 100.0
X Ray Diffraction 4.876 33.7495 2931 171 2760 0.1717 0.204 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 60.2
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.076
f_dihedral_angle_d 15.287
f_angle_d 1.122
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4397
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 48

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: dev_1032) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1032) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection