X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 290.0
Details Microlytics MCSG1 screen F1: 20% PEG 5000MME, 100mM BisTris pH 6.5; ButhA.17991.a.A1.PW33475 at 20mg/ml with 2.5mM NAD and 2.5mM Glu; cryo: 20% EG; tray 257704f1, puck smx9-3

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.49 α = 90
b = 93.52 β = 106.23
c = 158.37 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 RIGAKU SATURN 944+ -- 2014-09-18
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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 50 96.7 0.083 -- -- 6.6 -- 174736 -- -3.0 22.28
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)
2.0 2.05 92.6 0.392 -- 3.3 4.6 --

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 2.0 45.842 -- 1.34 -- 174723 1995 96.75 -- 0.1766 0.1761 0.2222 Random selection
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 2.0 2.05 -- 130 11711 0.1864 0.2402 -- 93.0
X Ray Diffraction 2.05 2.1055 -- 150 12090 0.199 0.2598 -- 95.0
X Ray Diffraction 2.1055 2.1674 -- 137 12281 0.2091 0.2658 -- 97.0
X Ray Diffraction 2.1674 2.2374 -- 132 11953 0.2585 0.3204 -- 94.0
X Ray Diffraction 2.2374 2.3173 -- 138 11703 0.322 0.4281 -- 92.0
X Ray Diffraction 2.3173 2.4101 -- 147 12356 0.2077 0.2409 -- 97.0
X Ray Diffraction 2.4101 2.5198 -- 139 12457 0.186 0.2541 -- 98.0
X Ray Diffraction 2.5198 2.6526 -- 141 12423 0.1826 0.2609 -- 98.0
X Ray Diffraction 2.6526 2.8188 -- 151 12473 0.1715 0.2238 -- 98.0
X Ray Diffraction 2.8188 3.0364 -- 143 12570 0.1774 0.2447 -- 98.0
X Ray Diffraction 3.0364 3.3419 -- 142 12592 0.1694 0.2112 -- 99.0
X Ray Diffraction 3.3419 3.8252 -- 149 12610 0.1555 0.2062 -- 99.0
X Ray Diffraction 3.8252 4.8186 -- 147 12654 0.1305 0.1616 -- 99.0
X Ray Diffraction 4.8186 45.8545 -- 149 12855 0.147 0.1597 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.5192
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.899
f_angle_d 1.033
f_chiral_restr 0.039
f_plane_restr 0.005
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18661
Nucleic Acid Atoms 0
Heterogen Atoms 348
Solvent Atoms 1643

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHASER phasing
ARP model building
Coot model building
PHENIX refinement
PDB_EXTRACT data extraction