X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 9
Temperature 291.0
Details 40% PEG 1000, 0.1M lithium chloride, 0.1M TAPS, pH 9.0 , Microbatch crystallization under oil, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.09 α = 90
b = 56.82 β = 90
c = 105.6 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2012-08-09
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.97915 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
1.99 50 94.4 0.1 -- -- 3.2 37872 35751 0.0 0.0 23.73
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)
1.99 2.06 80.3 0.331 -- 3.0 2.7 3796

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 2.002 30.139 -- 0.65 -- 35590 1808 94.59 -- 0.177 0.176 0.202 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 2.002 2.056 -- 101 2262 0.198 0.26 -- 82.0
X Ray Diffraction 2.056 2.117 -- 145 2507 0.186 0.187 -- 91.0
X Ray Diffraction 2.117 2.185 -- 119 2570 0.18 0.225 -- 91.0
X Ray Diffraction 2.185 2.263 -- 117 2537 0.193 0.264 -- 93.0
X Ray Diffraction 2.263 2.354 -- 171 2520 0.175 0.256 -- 93.0
X Ray Diffraction 2.354 2.461 -- 140 2573 0.176 0.236 -- 93.0
X Ray Diffraction 2.461 2.591 -- 150 2558 0.184 0.211 -- 95.0
X Ray Diffraction 2.591 2.753 -- 165 2665 0.191 0.232 -- 97.0
X Ray Diffraction 2.753 2.965 -- 151 2669 0.196 0.26 -- 98.0
X Ray Diffraction 2.965 3.263 -- 140 2720 0.191 0.235 -- 99.0
X Ray Diffraction 3.263 3.735 -- 148 2745 0.164 0.167 -- 99.0
X Ray Diffraction 3.735 4.702 -- 130 2735 0.141 0.131 -- 100.0
X Ray Diffraction 4.702 30.142 -- 131 2721 0.184 0.183 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.95
Anisotropic B[1][1] 1.206
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.477
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.683
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.531
f_plane_restr 0.006
f_chiral_restr 0.088
f_angle_d 1.194
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2358
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 177

Software

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