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 = 78.3 α = 90
b = 153.52 β = 90
c = 52.83 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
1.9 30 97.5 0.121 -- -- 6.0 51152 49866 -- -3.0 22.329
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)
1.9 1.95 95.5 0.652 -- 2.73 5.2 3707

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 1.9 29.106 -- 2.0 -- 49808 1987 97.53 -- 0.1606 0.1593 0.1932 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 1.9 1.9475 3424 136 3288 0.1986 0.2409 -- 96.0
X Ray Diffraction 1.9475 2.0001 3445 137 3308 0.1838 0.2257 -- 96.0
X Ray Diffraction 2.0001 2.059 3485 139 3346 0.1736 0.2185 -- 97.0
X Ray Diffraction 2.059 2.1254 3476 139 3337 0.1687 0.2106 -- 96.0
X Ray Diffraction 2.1254 2.2014 3491 140 3351 0.1568 0.2196 -- 96.0
X Ray Diffraction 2.2014 2.2895 3513 141 3372 0.1524 0.1955 -- 98.0
X Ray Diffraction 2.2895 2.3936 3534 139 3395 0.1526 0.1993 -- 98.0
X Ray Diffraction 2.3936 2.5198 3536 142 3394 0.1614 0.2033 -- 98.0
X Ray Diffraction 2.5198 2.6775 3560 142 3418 0.1542 0.1748 -- 98.0
X Ray Diffraction 2.6775 2.8841 3595 144 3451 0.1594 0.219 -- 99.0
X Ray Diffraction 2.8841 3.174 3582 143 3439 0.1594 0.1836 -- 98.0
X Ray Diffraction 3.174 3.6326 3632 144 3488 0.1534 0.18 -- 99.0
X Ray Diffraction 3.6326 4.5738 3675 147 3528 0.1373 0.1685 -- 99.0
X Ray Diffraction 4.5738 29.109 3860 154 3706 0.171 0.1819 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 18.1009
Anisotropic B[1][1] 1.0835
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.5926
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5092
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.811
f_plane_restr 0.005
f_chiral_restr 0.073
f_angle_d 1.049
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4796
Nucleic Acid Atoms 0
Heterogen Atoms 131
Solvent Atoms 568

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