X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 8
Temperature 277.0
Details 20% PEG 4000, 0.1M magnesium sulfate, 0.1M Tris-HCl, pH 8.0, Microbatch crystallization under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.98 α = 90
b = 45.47 β = 107.17
c = 63.15 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 MAR CCD 165 mm -- 2012-09-21
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.97885 NSLS X4C

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
2.3 50 98.9 0.071 -- -- 3.7 27096 26798 0.0 0.0 28.07
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)
2.3 2.37 99.9 0.146 -- 8.8 3.8 2694

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 2.294 35.537 -- 1.15 -- 26546 1316 97.99 -- 0.196 0.194 0.236 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 2.294 2.386 -- 120 2814 0.194 0.257 -- 98.0
X Ray Diffraction 2.386 2.494 -- 171 2857 0.186 0.255 -- 100.0
X Ray Diffraction 2.494 2.626 -- 168 2792 0.203 0.264 -- 99.0
X Ray Diffraction 2.626 2.79 -- 146 2707 0.234 0.363 -- 95.0
X Ray Diffraction 2.79 3.006 -- 142 2899 0.224 0.274 -- 100.0
X Ray Diffraction 3.006 3.308 -- 115 2881 0.216 0.247 -- 100.0
X Ray Diffraction 3.308 3.786 -- 145 2731 0.193 0.227 -- 95.0
X Ray Diffraction 3.786 4.768 -- 151 2770 0.16 0.18 -- 97.0
X Ray Diffraction 4.768 35.541 -- 158 2779 0.186 0.206 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.025
Anisotropic B[1][1] -1.868
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.09
Anisotropic B[2][2] -10.693
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.561
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.113
f_plane_restr 0.005
f_chiral_restr 0.09
f_angle_d 1.375
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2419
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 93

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MolRep Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement