X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.8
Details 60MM NA2HPO4 PH 6.0; 15% PEG1000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.32 α = 90
b = 87.35 β = 91.23
c = 61.88 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 -- -- 2008-12-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- DIAMOND I04

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 43.67 95.7 0.09 -- -- 3.7 -- 59656 -- 3.0 10.42
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 1.63 93.8 0.65 -- 1.9 3.7 --

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 1.548 43.675 -- 1.99 -- 59636 2899 95.67 -- 0.1979 0.1961 0.2349 --
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 1.5477 1.5731 -- 129 2585 0.249 0.2823 -- 93.0
X Ray Diffraction 1.5731 1.6002 -- 145 2632 0.2472 0.2943 -- 94.0
X Ray Diffraction 1.6002 1.6293 -- 133 2669 0.2392 0.2809 -- 94.0
X Ray Diffraction 1.6293 1.6607 -- 127 2661 0.2238 0.3059 -- 95.0
X Ray Diffraction 1.6607 1.6945 -- 126 2648 0.2181 0.2811 -- 94.0
X Ray Diffraction 1.6945 1.7314 -- 136 2672 0.2182 0.256 -- 95.0
X Ray Diffraction 1.7314 1.7717 -- 146 2670 0.2044 0.3013 -- 94.0
X Ray Diffraction 1.7717 1.816 -- 151 2691 0.2021 0.227 -- 95.0
X Ray Diffraction 1.816 1.8651 -- 150 2640 0.1966 0.2728 -- 95.0
X Ray Diffraction 1.8651 1.92 -- 131 2704 0.201 0.2744 -- 95.0
X Ray Diffraction 1.92 1.9819 -- 136 2704 0.1898 0.2519 -- 96.0
X Ray Diffraction 1.9819 2.0528 -- 174 2681 0.1816 0.2131 -- 96.0
X Ray Diffraction 2.0528 2.135 -- 130 2727 0.1844 0.2488 -- 95.0
X Ray Diffraction 2.135 2.2321 -- 127 2707 0.1841 0.2328 -- 96.0
X Ray Diffraction 2.2321 2.3498 -- 122 2723 0.1883 0.2245 -- 97.0
X Ray Diffraction 2.3498 2.497 -- 147 2746 0.1951 0.2698 -- 97.0
X Ray Diffraction 2.497 2.6898 -- 121 2754 0.1958 0.2449 -- 97.0
X Ray Diffraction 2.6898 2.9604 -- 148 2758 0.2036 0.2116 -- 98.0
X Ray Diffraction 2.9604 3.3886 -- 132 2759 0.1831 0.1988 -- 97.0
X Ray Diffraction 3.3886 4.2688 -- 128 2802 0.1679 0.1883 -- 98.0
X Ray Diffraction 4.2688 43.6924 -- 160 2804 0.1903 0.1954 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.04
Anisotropic B[1][1] 3.8374
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.5125
Anisotropic B[2][2] -4.9577
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.1203
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 17.767
f_angle_d 1.115
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3462
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 627

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
AMORE Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
AMORE model building