X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 291.0
Details 1.3-1.5 M ammonium sulfate, pH 5.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122 α = 90
b = 122 β = 90
c = 68 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-05-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97580 APS 24-ID-C

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
1.4 50 99.8 0.053 -- -- 5.1 58855 58855 -- -3.0 --
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)
1.4 1.45 100.0 0.47 -- -- 5.0 5791

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 1.4 39.934 -- 1.0 58855 56903 2810 96.61 -- 0.1496 0.1489 0.1643 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 1.4 1.4242 -- 130 2412 0.2233 0.246 -- 88.0
X Ray Diffraction 1.4242 1.4501 -- 140 2505 0.1933 0.2299 -- 91.0
X Ray Diffraction 1.4501 1.478 -- 144 2533 0.1758 0.2033 -- 93.0
X Ray Diffraction 1.478 1.5081 -- 139 2584 0.1579 0.169 -- 94.0
X Ray Diffraction 1.5081 1.5409 -- 136 2630 0.1438 0.1592 -- 96.0
X Ray Diffraction 1.5409 1.5768 -- 137 2650 0.1496 0.1788 -- 96.0
X Ray Diffraction 1.5768 1.6162 -- 145 2648 0.1467 0.1627 -- 96.0
X Ray Diffraction 1.6162 1.6599 -- 140 2682 0.1343 0.1431 -- 97.0
X Ray Diffraction 1.6599 1.7088 -- 143 2671 0.1341 0.1521 -- 97.0
X Ray Diffraction 1.7088 1.7639 -- 139 2717 0.1345 0.1503 -- 98.0
X Ray Diffraction 1.7639 1.827 -- 129 2744 0.1269 0.125 -- 98.0
X Ray Diffraction 1.827 1.9001 -- 141 2728 0.1269 0.1369 -- 98.0
X Ray Diffraction 1.9001 1.9866 -- 135 2766 0.1197 0.137 -- 99.0
X Ray Diffraction 1.9866 2.0913 -- 125 2784 0.1277 0.1492 -- 99.0
X Ray Diffraction 2.0913 2.2223 -- 132 2807 0.1263 0.1573 -- 99.0
X Ray Diffraction 2.2223 2.3939 -- 154 2783 0.125 0.1244 -- 99.0
X Ray Diffraction 2.3939 2.6348 -- 145 2821 0.1348 0.1487 -- 99.0
X Ray Diffraction 2.6348 3.0159 -- 134 2846 0.1496 0.172 -- 100.0
X Ray Diffraction 3.0159 3.7992 -- 153 2893 0.1531 0.1699 -- 100.0
X Ray Diffraction 3.7992 39.9501 -- 169 2889 0.1893 0.1973 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.6062
Anisotropic B[1][1] 0.1479
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1479
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2957
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.314
f_chiral_restr 0.07
f_bond_d 0.009
f_plane_restr 0.006
f_angle_d 1.282
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1731
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 182

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing