X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.43 α = 90
b = 74.43 β = 90
c = 105.4 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-03
Diffraction Radiation
Monochromator Protocol
Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.08090 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
2.05 50 99.9 0.072 0.072 -- 9.3 -- 20690 0.0 -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)
2.05 2.12 100.0 0.495 0.495 4.079 9.5 --

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 2.051 28.144 -- 0.11 -- 18131 918 94.51 -- 0.1699 0.1675 0.2184 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 2.0512 2.1593 -- 109 2242 0.1862 0.2454 -- 88.0
X Ray Diffraction 2.1593 2.2945 -- 124 2214 0.203 0.2827 -- 87.0
X Ray Diffraction 2.2945 2.4716 -- 137 2398 0.1728 0.2381 -- 94.0
X Ray Diffraction 2.4716 2.7201 -- 147 2451 0.1667 0.211 -- 96.0
X Ray Diffraction 2.7201 3.1133 -- 143 2522 0.1687 0.2277 -- 97.0
X Ray Diffraction 3.1133 3.9207 -- 138 2614 0.1536 0.2187 -- 99.0
X Ray Diffraction 3.9207 28.1462 -- 120 2772 0.1587 0.1786 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.1221
Anisotropic B[1][1] 5.6971
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.6971
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.3942
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.005
f_plane_restr 0.005
f_chiral_restr 0.056
f_angle_d 0.906
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1656
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 234

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.6_289) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
MOLREP molecular replacement
HKL data reduction