X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.16 α = 90
b = 70.66 β = 99.16
c = 108.41 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 315 -- 2006-12-14
Diffraction Radiation
Monochromator Protocol
Si-111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97910 APS 19-ID

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
3 50 99.7 0.1 -- -- 8.3 30762 30762 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)
3.0 3.11 99.5 0.382 -- -- 8.1 3050

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 3.0 42.662 -- 1.91 -- 30762 2988 99.39 -- 0.3225 0.3211 0.3487 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 3.0 3.0499 -- 108 2608 0.4075 0.498 -- 96.0
X Ray Diffraction 3.0499 3.1025 -- 151 2698 0.4076 0.4366 -- 100.0
X Ray Diffraction 3.1025 3.1589 -- 143 2697 0.3983 0.392 -- 100.0
X Ray Diffraction 3.1589 3.2196 -- 145 2725 0.4053 0.4523 -- 100.0
X Ray Diffraction 3.2196 3.2853 -- 138 2693 0.3695 0.4011 -- 100.0
X Ray Diffraction 3.2853 3.3567 -- 123 2760 0.3905 0.4018 -- 100.0
X Ray Diffraction 3.3567 3.4347 -- 128 2651 0.3653 0.3592 -- 100.0
X Ray Diffraction 3.4347 3.5206 -- 137 2725 0.3577 0.4318 -- 100.0
X Ray Diffraction 3.5206 3.6157 -- 153 2675 0.3185 0.3383 -- 100.0
X Ray Diffraction 3.6157 3.7221 -- 126 2773 0.3354 0.3663 -- 100.0
X Ray Diffraction 3.7221 3.8421 -- 145 2625 0.3246 0.3868 -- 100.0
X Ray Diffraction 3.8421 3.9794 -- 135 2748 0.3333 0.2655 -- 100.0
X Ray Diffraction 3.9794 4.1386 -- 165 2705 0.3216 0.3094 -- 100.0
X Ray Diffraction 4.1386 4.3268 -- 156 2644 0.3029 0.2983 -- 100.0
X Ray Diffraction 4.3268 4.5546 -- 153 2707 0.2804 0.2679 -- 100.0
X Ray Diffraction 4.5546 4.8396 -- 139 2708 0.2351 0.298 -- 100.0
X Ray Diffraction 4.8396 5.2127 -- 166 2689 0.2994 0.3077 -- 100.0
X Ray Diffraction 5.2127 5.7361 -- 135 2712 0.2956 0.4199 -- 100.0
X Ray Diffraction 5.7361 6.5636 -- 168 2688 0.3234 0.3896 -- 100.0
X Ray Diffraction 6.5636 8.2596 -- 135 2712 0.3296 0.3811 -- 100.0
X Ray Diffraction 8.2596 42.6658 -- 139 2589 0.2548 0.3099 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.6175
Anisotropic B[1][1] -7.2698
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -11.9263
Anisotropic B[2][2] -4.114
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.8191
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.432
f_plane_restr 0.003
f_chiral_restr 0.072
f_angle_d 0.912
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12360
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
In-house software Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
HKL3000 Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction