X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 283.0
Details Compound soaked into crystal grown in equal volume of 500mM MES buffer (pH 6.0) and 25% MPD, vapor diffusion, hanging drop, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.79 α = 90
b = 73.5 β = 90
c = 104.16 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 QUANTUM 315r -- 2012-07-11
Diffraction Radiation
Monochromator Protocol
KOHZU DUAL DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1

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
1.51 31.4 99.1 0.043 -- -- 4.0 61321 61321 1.35 2.2 17.7
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)
1.51 1.55 97.7 0.4 -- 2.2 2.6 4240

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 1.51 31.4 -- 1.35 61321 61321 3103 99.01 -- 0.1469 0.1452 0.178 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 1.51 1.5336 -- 148 2442 0.2439 0.3311 -- 94.0
X Ray Diffraction 1.5336 1.5587 -- 124 2534 0.2048 0.2642 -- 97.0
X Ray Diffraction 1.5587 1.5856 -- 128 2641 0.1703 0.1854 -- 99.0
X Ray Diffraction 1.5856 1.6145 -- 143 2615 0.1462 0.1787 -- 100.0
X Ray Diffraction 1.6145 1.6455 -- 155 2606 0.1379 0.1808 -- 100.0
X Ray Diffraction 1.6455 1.6791 -- 141 2649 0.136 0.1756 -- 100.0
X Ray Diffraction 1.6791 1.7156 -- 134 2649 0.1256 0.1754 -- 100.0
X Ray Diffraction 1.7156 1.7555 -- 128 2671 0.1315 0.1869 -- 100.0
X Ray Diffraction 1.7555 1.7994 -- 123 2658 0.1285 0.1706 -- 100.0
X Ray Diffraction 1.7994 1.848 -- 140 2618 0.1347 0.1729 -- 100.0
X Ray Diffraction 1.848 1.9024 -- 154 2673 0.1426 0.1705 -- 100.0
X Ray Diffraction 1.9024 1.9638 -- 147 2638 0.1401 0.2058 -- 100.0
X Ray Diffraction 1.9638 2.034 -- 152 2634 0.1312 0.1537 -- 100.0
X Ray Diffraction 2.034 2.1154 -- 139 2648 0.1346 0.1684 -- 99.0
X Ray Diffraction 2.1154 2.2117 -- 147 2634 0.1319 0.189 -- 99.0
X Ray Diffraction 2.2117 2.3282 -- 121 2677 0.1336 0.1713 -- 99.0
X Ray Diffraction 2.3282 2.474 -- 144 2631 0.1388 0.1669 -- 99.0
X Ray Diffraction 2.474 2.665 -- 153 2653 0.14 0.1467 -- 99.0
X Ray Diffraction 2.665 2.933 -- 145 2668 0.1543 0.1727 -- 99.0
X Ray Diffraction 2.933 3.357 -- 143 2699 0.1465 0.1877 -- 99.0
X Ray Diffraction 3.357 4.2278 -- 151 2738 0.1396 0.1559 -- 100.0
X Ray Diffraction 4.2278 31.4 -- 143 2842 0.1647 0.2035 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8295
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.017
f_chiral_restr 0.102
f_dihedral_angle_d 14.964
f_plane_restr 0.009
f_angle_d 1.542
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2328
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 325

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement version: dev_1391
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum