X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.7 α = 90
b = 92.7 β = 90
c = 130.8 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Collimating Mirror 2009-08-14
Diffraction Radiation
Monochromator Protocol
Bartels SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA

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
1.5 50 99.9 -- 0.079 -- 20.7 53702 53702 -- -- --
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)
1.5 1.53 99.5 -- 0.499 6.6 18.5 2620

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 1.5 40.14 -- 0.0 54982 52333 2649 97.59 0.1423 0.1423 0.1416 0.1562 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 1.5 1.5273 -- 121 2444 0.1714 0.207 -- 93.0
X Ray Diffraction 1.5273 1.5567 -- 131 2468 0.1631 0.1814 -- 94.0
X Ray Diffraction 1.5567 1.5885 -- 146 2468 0.1525 0.1776 -- 95.0
X Ray Diffraction 1.5885 1.623 -- 133 2507 0.1428 0.1609 -- 95.0
X Ray Diffraction 1.623 1.6607 -- 127 2535 0.1408 0.1766 -- 96.0
X Ray Diffraction 1.6607 1.7023 -- 133 2544 0.1395 0.1543 -- 96.0
X Ray Diffraction 1.7023 1.7483 -- 135 2566 0.139 0.1826 -- 97.0
X Ray Diffraction 1.7483 1.7998 -- 150 2558 0.1354 0.1764 -- 97.0
X Ray Diffraction 1.7998 1.8578 -- 130 2570 0.13 0.1526 -- 97.0
X Ray Diffraction 1.8578 1.9242 -- 150 2592 0.1312 0.1647 -- 98.0
X Ray Diffraction 1.9242 2.0013 -- 131 2640 0.1387 0.146 -- 99.0
X Ray Diffraction 2.0013 2.0924 -- 137 2648 0.1429 0.1895 -- 99.0
X Ray Diffraction 2.0924 2.2027 -- 147 2673 0.137 0.1642 -- 100.0
X Ray Diffraction 2.2027 2.3407 -- 141 2657 0.137 0.1423 -- 99.0
X Ray Diffraction 2.3407 2.5214 -- 150 2668 0.1405 0.1495 -- 99.0
X Ray Diffraction 2.5214 2.775 -- 148 2698 0.1421 0.1623 -- 100.0
X Ray Diffraction 2.775 3.1764 -- 142 2716 0.1402 0.1328 -- 100.0
X Ray Diffraction 3.1764 4.0014 -- 150 2781 0.1344 0.1494 -- 100.0
X Ray Diffraction 4.0014 40.1546 -- 147 2951 0.1531 0.1426 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.4543
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4543
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.9086
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 15.241
f_angle_d 1.054
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2428
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 442

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
MAR345dtb data collection