X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.17 α = 90
b = 153.25 β = 90
c = 52.72 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm Multilayer mirror, curved to focus in the vertical (R = 400 m) 2010-03-26
Diffraction Radiation
Monochromator Protocol
Bent Si (111) crystal, horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.03796 MAX II I911-2

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
1.68 30 95.8 0.067 -- -- 5.9 73143 70045 -- -3.0 25.996
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)
1.68 1.72 90.3 0.688 -- 2.23 4.8 5325

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 1.68 29.053 -- 1.99 -- 69982 2799 95.8 -- 0.1649 0.1638 0.1918 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 1.68 1.709 3239 129 3110 0.2811 0.2956 -- 90.0
X Ray Diffraction 1.709 1.74 3299 132 3167 0.249 0.2822 -- 92.0
X Ray Diffraction 1.74 1.7735 3328 134 3194 0.2297 0.227 -- 93.0
X Ray Diffraction 1.7735 1.8097 3351 134 3217 0.2132 0.2585 -- 93.0
X Ray Diffraction 1.8097 1.849 3403 136 3267 0.207 0.2667 -- 94.0
X Ray Diffraction 1.849 1.892 3405 136 3269 0.1823 0.2469 -- 94.0
X Ray Diffraction 1.892 1.9394 3413 137 3276 0.1626 0.1804 -- 95.0
X Ray Diffraction 1.9394 1.9918 3453 138 3315 0.152 0.1932 -- 96.0
X Ray Diffraction 1.9918 2.0504 3498 140 3358 0.1485 0.1727 -- 96.0
X Ray Diffraction 2.0504 2.1165 3468 139 3329 0.1541 0.2228 -- 96.0
X Ray Diffraction 2.1165 2.1922 3497 139 3358 0.1578 0.1852 -- 97.0
X Ray Diffraction 2.1922 2.2799 3499 139 3360 0.1527 0.2129 -- 97.0
X Ray Diffraction 2.2799 2.3836 3566 143 3423 0.154 0.1952 -- 97.0
X Ray Diffraction 2.3836 2.5092 3545 142 3403 0.1561 0.2186 -- 97.0
X Ray Diffraction 2.5092 2.6663 3576 143 3433 0.1536 0.1858 -- 98.0
X Ray Diffraction 2.6663 2.872 3617 145 3472 0.1594 0.2145 -- 99.0
X Ray Diffraction 2.872 3.1607 3612 145 3467 0.1589 0.1769 -- 98.0
X Ray Diffraction 3.1607 3.6174 3652 146 3506 0.1519 0.1811 -- 99.0
X Ray Diffraction 3.6174 4.5547 3694 147 3547 0.1382 0.1381 -- 99.0
X Ray Diffraction 4.5547 29.0575 3867 155 3712 0.1807 0.1852 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 21.9192
Anisotropic B[1][1] 2.0355
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.2067
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1712
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.34
f_plane_restr 0.007
f_chiral_restr 0.09
f_angle_d 1.3
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4712
Nucleic Acid Atoms 0
Heterogen Atoms 129
Solvent Atoms 542

Software

Computing
Computing Package Purpose
MARCCD Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction