X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 1.45M SODIUM CITRATE, 0.2M NDSB-201, pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.13 α = 90
b = 128.13 β = 90
c = 63.08 γ = 90
Symmetry
Space Group P 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 294
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2011-02-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A -- PHOTON FACTORY AR-NW12A

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
1.78 28.65 94.2 0.07 -- -- 4.7 -- 91927 -- 0.0 17.33
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)
1.78 1.81 98.1 0.46 -- 2.7 3.8 --

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 1.783 28.651 -- 0.0 -- 91927 4592 94.16 -- 0.1964 0.1951 0.2206 --
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 1.7834 1.8471 -- 440 8018 0.2243 0.2692 -- 87.0
X Ray Diffraction 1.8471 1.921 -- 400 8430 0.2234 0.2581 -- 91.0
X Ray Diffraction 1.921 2.0085 -- 472 8577 0.2155 0.2414 -- 93.0
X Ray Diffraction 2.0085 2.1143 -- 483 8628 0.2065 0.2522 -- 94.0
X Ray Diffraction 2.1143 2.2467 -- 459 8690 0.1959 0.2463 -- 94.0
X Ray Diffraction 2.2467 2.4201 -- 424 8773 0.1949 0.2369 -- 94.0
X Ray Diffraction 2.4201 2.6635 -- 451 8836 0.2148 0.2623 -- 96.0
X Ray Diffraction 2.6635 3.0485 -- 471 8955 0.2169 0.2283 -- 96.0
X Ray Diffraction 3.0485 3.8394 -- 452 9082 0.1762 0.1915 -- 97.0
X Ray Diffraction 3.8394 28.6546 -- 540 9346 0.1741 0.1836 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.25
Anisotropic B[1][1] -1.0086
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0086
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.0173
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.07
f_bond_d 0.007
f_angle_d 1.059
f_dihedral_angle_d 14.735
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6440
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 866

Software

Computing
Computing Package Purpose
HKL2000 Data Reduction (intensity integration)
HKL2000 Data Reduction (data scaling)
SOLVE RESOLVE Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
SOLVE version: RESOLVE model building