X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.2
Details pH 6.2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.23 α = 90
b = 60.59 β = 90
c = 87.52 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2009-05-14
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
1.19 26.29 93.4 0.06 -- -- 4.6 -- 64405 -- 5.0 8.39
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)
1.19 1.26 90.4 0.24 -- 5.14 3.8 --

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 1.193 26.286 -- 2.0 -- 64403 3251 93.44 -- 0.1414 0.14 0.1671 --
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 1.1925 1.2103 -- 115 2162 0.1966 0.2337 -- 76.0
X Ray Diffraction 1.2103 1.2292 -- 165 2610 0.1663 0.1944 -- 95.0
X Ray Diffraction 1.2292 1.2494 -- 159 2705 0.1357 0.1646 -- 97.0
X Ray Diffraction 1.2494 1.2709 -- 135 2702 0.1233 0.1542 -- 97.0
X Ray Diffraction 1.2709 1.294 -- 148 2721 0.1245 0.1646 -- 96.0
X Ray Diffraction 1.294 1.3189 -- 141 2735 0.1227 0.1556 -- 97.0
X Ray Diffraction 1.3189 1.3458 -- 153 2727 0.1221 0.1578 -- 96.0
X Ray Diffraction 1.3458 1.3751 -- 139 2725 0.1168 0.162 -- 98.0
X Ray Diffraction 1.3751 1.4071 -- 146 2708 0.1133 0.1353 -- 96.0
X Ray Diffraction 1.4071 1.4423 -- 135 2747 0.1165 0.1657 -- 97.0
X Ray Diffraction 1.4423 1.4813 -- 157 2738 0.113 0.1513 -- 97.0
X Ray Diffraction 1.4813 1.5248 -- 148 2693 0.1056 0.1442 -- 96.0
X Ray Diffraction 1.5248 1.5741 -- 134 2733 0.1068 0.1343 -- 96.0
X Ray Diffraction 1.5741 1.6303 -- 131 2744 0.1069 0.1471 -- 96.0
X Ray Diffraction 1.6303 1.6956 -- 126 2753 0.1148 0.1476 -- 96.0
X Ray Diffraction 1.6956 1.7727 -- 138 2699 0.123 0.1677 -- 95.0
X Ray Diffraction 1.7727 1.8662 -- 128 2725 0.1324 0.1491 -- 95.0
X Ray Diffraction 1.8662 1.9831 -- 128 2680 0.1315 0.2103 -- 94.0
X Ray Diffraction 1.9831 2.1361 -- 166 2659 0.1385 0.1495 -- 93.0
X Ray Diffraction 2.1361 2.3509 -- 146 2636 0.1365 0.1544 -- 92.0
X Ray Diffraction 2.3509 2.6908 -- 137 2618 0.1558 0.1739 -- 90.0
X Ray Diffraction 2.6908 3.389 -- 161 2568 0.1596 0.1896 -- 88.0
X Ray Diffraction 3.389 26.2924 -- 115 2364 0.1843 0.1815 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.2999
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.1044
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.4043
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.074
f_dihedral_angle_d 13.387
f_angle_d 1.397
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1782
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 319

Software

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