X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.1M MES pH6.5, 0.75M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 208.12 α = 90
b = 208.12 β = 90
c = 182.13 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2009-03-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00 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
4.5 30.04 100.0 0.078 -- -- 15.5 -- 14397 -- -- 154.7
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)
4.5 4.66 100.0 0.592 -- 4.9 10.9 1396

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 4.515 30.039 -- 1.34 -- 14115 710 99.84 -- 0.3263 0.3258 0.3376 --
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 4.5151 4.8624 -- 165 2585 0.3488 0.3622 -- 99.0
X Ray Diffraction 4.8624 5.3492 -- 131 2624 0.3187 0.3075 -- 100.0
X Ray Diffraction 5.3492 6.1176 -- 141 2657 0.3002 0.3579 -- 100.0
X Ray Diffraction 6.1176 7.6861 -- 155 2672 0.3538 0.3563 -- 100.0
X Ray Diffraction 7.6861 30.04 -- 118 2867 0.3188 0.3208 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 271.893
Anisotropic B[1][1] 1.5731
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.5731
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.1463
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.104
f_dihedral_angle_d 16.226
f_angle_d 1.566
f_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.6
Luzzati Sigma A (Observed) 1.38
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.76
Luzzati Sigma A (R-Free Set) 1.85
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4135
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER model building
ADSC version: Quantum data collection