X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 298.0
Details PEG 3350, sodium malonate, MnCl2, pH 7.0, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.93 α = 90
b = 344.74 β = 91.95
c = 55.23 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
PIXEL DECTRIS PILATUS 6M -- 2012-03-09
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.033 SSRL BL12-2

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
2.42 38.31 95.5 -- 0.072 -- 3.1 74318 74318 -- -3.0 --
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)
2.42 2.55 80.1 0.482 0.482 1.6 2.6 --

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 2.42 37.44 -- 1.36 77751 74237 1992 95.5 -- 0.195 0.194 0.237 --
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 2.4188 2.4793 -- 95 3474 0.2966 0.3562 -- 64.0
X Ray Diffraction 2.4793 2.5463 -- 137 5131 0.2842 0.3558 -- 96.0
X Ray Diffraction 2.5463 2.6213 -- 145 5382 0.2653 0.3267 -- 99.0
X Ray Diffraction 2.6213 2.7058 -- 140 5290 0.2579 0.3139 -- 99.0
X Ray Diffraction 2.7058 2.8025 -- 157 5282 0.2497 0.2915 -- 99.0
X Ray Diffraction 2.8025 2.9147 -- 142 5418 0.2446 0.3032 -- 98.0
X Ray Diffraction 2.9147 3.0473 -- 147 5306 0.2424 0.3107 -- 98.0
X Ray Diffraction 3.0473 3.2079 -- 140 5278 0.2251 0.3196 -- 99.0
X Ray Diffraction 3.2079 3.4087 -- 157 5259 0.2104 0.2799 -- 98.0
X Ray Diffraction 3.4087 3.6717 -- 151 5287 0.1937 0.2467 -- 97.0
X Ray Diffraction 3.6717 4.0408 -- 138 5285 0.1705 0.2141 -- 99.0
X Ray Diffraction 4.0408 4.6246 -- 147 5320 0.1396 0.1752 -- 98.0
X Ray Diffraction 4.6246 5.823 -- 149 5256 0.1437 0.1472 -- 98.0
X Ray Diffraction 5.823 37.4482 -- 147 5277 0.1769 0.2028 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.067
f_dihedral_angle_d 12.916
f_angle_d 0.951
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13261
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 490

Software

Computing
Computing Package Purpose
XDS Data Collection
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.16 data reduction