X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 20% PEG 3350, 0.2M Na2HPO4, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.52 α = 90
b = 69.21 β = 96.61
c = 67.19 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 ADSC QUANTUM 4r TOROIDAL MIRROR 2006-04-27
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3

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
1.45 25 99.7 0.077 -- -- 4.2 -- 69956 0.0 0.0 --
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)
1.45 1.47 100.0 0.537 -- -- 4.1 3472

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 1.45 21.779 0.0 1.89 69847 69847 3524 99.49 -- 0.171 0.1694 0.2003 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 1.45 1.4694 -- 144 2598 0.2367 0.265 -- 99.0
X Ray Diffraction 1.4694 1.4904 -- 134 2680 0.2287 0.2592 -- 100.0
X Ray Diffraction 1.4904 1.5126 -- 127 2675 0.2162 0.2377 -- 100.0
X Ray Diffraction 1.5126 1.5363 -- 129 2649 0.1992 0.2343 -- 100.0
X Ray Diffraction 1.5363 1.5614 -- 152 2628 0.1985 0.2387 -- 100.0
X Ray Diffraction 1.5614 1.5884 -- 164 2644 0.1866 0.2241 -- 100.0
X Ray Diffraction 1.5884 1.6172 -- 137 2656 0.1855 0.209 -- 100.0
X Ray Diffraction 1.6172 1.6483 -- 133 2661 0.1806 0.2162 -- 100.0
X Ray Diffraction 1.6483 1.682 -- 139 2684 0.1772 0.2155 -- 100.0
X Ray Diffraction 1.682 1.7185 -- 141 2622 0.1712 0.2186 -- 100.0
X Ray Diffraction 1.7185 1.7585 -- 159 2621 0.1732 0.2114 -- 99.0
X Ray Diffraction 1.7585 1.8024 -- 140 2651 0.1699 0.2186 -- 100.0
X Ray Diffraction 1.8024 1.8511 -- 142 2638 0.1748 0.1994 -- 99.0
X Ray Diffraction 1.8511 1.9056 -- 125 2632 0.1891 0.2001 -- 99.0
X Ray Diffraction 1.9056 1.967 -- 141 2653 0.1999 0.2983 -- 99.0
X Ray Diffraction 1.967 2.0373 -- 139 2664 0.1645 0.2159 -- 100.0
X Ray Diffraction 2.0373 2.1188 -- 145 2610 0.1645 0.1983 -- 99.0
X Ray Diffraction 2.1188 2.2151 -- 148 2666 0.1744 0.2282 -- 99.0
X Ray Diffraction 2.2151 2.3318 -- 142 2640 0.1786 0.2127 -- 99.0
X Ray Diffraction 2.3318 2.4777 -- 136 2679 0.1627 0.1935 -- 100.0
X Ray Diffraction 2.4777 2.6687 -- 130 2653 0.1636 0.2051 -- 100.0
X Ray Diffraction 2.6687 2.9367 -- 152 2696 0.1673 0.1955 -- 100.0
X Ray Diffraction 2.9367 3.3603 -- 145 2679 0.1582 0.1837 -- 100.0
X Ray Diffraction 3.3603 4.2285 -- 135 2621 0.1332 0.1436 -- 97.0
X Ray Diffraction 4.2285 21.7816 -- 145 2723 0.1498 0.1521 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.5475
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.873
f_plane_restr 0.005
f_chiral_restr 0.076
f_angle_d 1.13
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3077
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 753

Software

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction