X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 0.1M HEPES (pH 7.5), 50mM CdSO4, 1.0M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.97 α = 90
b = 61.13 β = 90
c = 70.39 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2012-10-23
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9500 Photon Factory BL-17A

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
1.07 50 97.5 0.051 -- -- 7.3 32553 31739 3.0 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)
1.07 1.11 95.3 0.889 -- 3.0 7.1 3147

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
SAD 1.071 28.038 -- 0.81 32553 31032 1676 97.45 -- 0.1839 0.1831 0.1986 --
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 1.071 1.1028 -- 138 2480 0.2743 0.2894 -- 95.0
X Ray Diffraction 1.1028 1.1384 -- 136 2498 0.205 0.2425 -- 96.0
X Ray Diffraction 1.1384 1.1791 -- 138 2502 0.1711 0.2203 -- 96.0
X Ray Diffraction 1.1791 1.2263 -- 131 2542 0.1666 0.1852 -- 97.0
X Ray Diffraction 1.2263 1.2821 -- 141 2540 0.1881 0.2193 -- 97.0
X Ray Diffraction 1.2821 1.3497 -- 142 2583 0.1558 0.1663 -- 97.0
X Ray Diffraction 1.3497 1.4342 -- 134 2576 0.1532 0.18 -- 99.0
X Ray Diffraction 1.4342 1.545 -- 139 2614 0.1519 0.1693 -- 98.0
X Ray Diffraction 1.545 1.7004 -- 146 2600 0.1516 0.1728 -- 99.0
X Ray Diffraction 1.7004 1.9464 -- 148 2652 0.1707 0.1823 -- 99.0
X Ray Diffraction 1.9464 2.4521 -- 147 2677 0.1856 0.155 -- 100.0
X Ray Diffraction 2.4521 28.0472 -- 136 2763 0.2023 0.2434 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.086
f_bond_d 0.007
f_angle_d 1.242
f_dihedral_angle_d 16.151
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 506
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 89

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASES phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
HKL-2000 data reduction
HKL-2000 data scaling