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_angle_d 1.115
f_chiral_restr 0.07
f_plane_restr 0.004
f_dihedral_angle_d 17.767
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

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
XSCALE data scaling
AMoRE phasing