X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES PH6.5, 2.0 M POTASSIUM ACETATE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.62 α = 90
b = 51.62 β = 90
c = 111.47 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 103
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2009-06-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A -- NSLS X29A

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
2.1 50 100.0 0.06 -- -- 11.9 -- 10569 -- 0.0 41.98
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)
2.1 2.18 100.0 0.42 -- 4.2 10.2 --

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 2.103 44.706 -- 0.65 -- 10026 987 95.2 -- 0.2271 0.2246 0.2497 --
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 2.1031 2.2139 -- 129 1147 0.2513 0.3049 -- 88.0
X Ray Diffraction 2.2139 2.3526 -- 136 1228 0.2351 0.3124 -- 91.0
X Ray Diffraction 2.3526 2.5343 -- 133 1229 0.2357 0.3081 -- 94.0
X Ray Diffraction 2.5343 2.7893 -- 140 1300 0.2585 0.2775 -- 97.0
X Ray Diffraction 2.7893 3.1928 -- 148 1335 0.2613 0.3268 -- 98.0
X Ray Diffraction 3.1928 4.0222 -- 148 1356 0.2096 0.2479 -- 100.0
X Ray Diffraction 4.0222 44.716 -- 153 1444 0.2091 0.1968 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.4
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.059
f_dihedral_angle_d 13.029
f_angle_d 1.071
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 870
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 24

Software

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