X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.2
Temperature 293.0
Details 2.5M Sodium formate, 0.1M acetate buffer, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.87 α = 90
b = 97.87 β = 90
c = 170.57 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2007-10-13
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 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
1.95 19.86 97.1 -- -- -- -- 34855 34855 0.0 0.0 25.88
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)
1.95 2.06 98.8 -- -- -- -- --

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
MOLECULAR REPLACEMENT 1.95 19.855 -- 2.05 -- 34852 1743 97.2 -- 0.2069 0.2056 0.231 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 1.9501 2.0074 -- 144 2739 0.2409 0.2984 -- 99.0
X Ray Diffraction 2.0074 2.0721 -- 144 2744 0.2289 0.316 -- 99.0
X Ray Diffraction 2.0721 2.1461 -- 144 2731 0.2205 0.2614 -- 98.0
X Ray Diffraction 2.1461 2.2319 -- 146 2764 0.224 0.2286 -- 98.0
X Ray Diffraction 2.2319 2.3334 -- 144 2738 0.2147 0.2406 -- 98.0
X Ray Diffraction 2.3334 2.4562 -- 144 2743 0.2252 0.2979 -- 98.0
X Ray Diffraction 2.4562 2.6098 -- 144 2736 0.2302 0.2708 -- 98.0
X Ray Diffraction 2.6098 2.8107 -- 145 2755 0.2411 0.2643 -- 97.0
X Ray Diffraction 2.8107 3.0926 -- 145 2754 0.2378 0.255 -- 97.0
X Ray Diffraction 3.0926 3.538 -- 146 2766 0.201 0.2145 -- 96.0
X Ray Diffraction 3.538 4.4492 -- 147 2794 0.173 0.1871 -- 96.0
X Ray Diffraction 4.4492 19.856 -- 150 2845 0.1737 0.1936 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.2479
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.076
f_plane_restr 0.005
f_angle_d 1.176
f_dihedral_angle_d 14.822
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2912
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 101

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
MOLREP phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
XDS data reduction
XSCALE data scaling