X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1.4 M Sodium Citrate 50 mM Tris pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.22 α = 90
b = 41.27 β = 104.24
c = 72.08 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
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2010-12-10
Diffraction Radiation
Monochromator Protocol
Rigaku Varimax HR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.55 50 89.8 -- 0.048 -- 4.6 31577 31199 1.0 2.0 --
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)
1.55 1.61 85.4 0.283 -- -- 4.6 2974

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 1.549 30.533 -- 0.0 31577 31199 1989 88.51 0.1645 0.1633 0.1628 0.1908 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 1.5491 1.5879 -- 113 1864 0.3206 0.3582 -- 79.0
X Ray Diffraction 1.5879 1.6308 -- 133 1926 0.2622 0.2689 -- 82.0
X Ray Diffraction 1.6308 1.6788 -- 140 1967 0.2163 0.259 -- 85.0
X Ray Diffraction 1.6788 1.7329 -- 128 2023 0.178 0.2123 -- 86.0
X Ray Diffraction 1.7329 1.7949 -- 148 2028 0.1599 0.1804 -- 87.0
X Ray Diffraction 1.7949 1.8667 -- 127 2053 0.1377 0.2066 -- 88.0
X Ray Diffraction 1.8667 1.9517 -- 148 2082 0.1468 0.1652 -- 89.0
X Ray Diffraction 1.9517 2.0546 -- 149 2120 0.1527 0.1704 -- 90.0
X Ray Diffraction 2.0546 2.1832 -- 146 2139 0.1588 0.1863 -- 91.0
X Ray Diffraction 2.1832 2.3518 -- 145 2125 0.1575 0.1984 -- 91.0
X Ray Diffraction 2.3518 2.5883 -- 145 2165 0.1597 0.1677 -- 92.0
X Ray Diffraction 2.5883 2.9626 -- 148 2216 0.1642 0.2085 -- 93.0
X Ray Diffraction 2.9626 3.7315 -- 158 2225 0.1481 0.1781 -- 94.0
X Ray Diffraction 3.7315 30.5391 -- 161 2277 0.1574 0.18 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.4863
Anisotropic B[1][1] -1.0559
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1473
Anisotropic B[2][2] -0.3107
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.3665
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.08
f_plane_restr 0.005
f_chiral_restr 0.079
f_angle_d 1.125
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2060
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 243

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data reduction