X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 10-12mg/ml enzyme in 50mM NaPO4, 2mM EDTA, pH 6.5; and 10-15% polyethylene glycol (PEG) 2,000 monomethyl ester, 0.2-0.3M K2HPO4, 0.1M D,L-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.6 α = 90
b = 67.63 β = 106.13
c = 99.41 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2008-08-18
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 0.9500 NSLS X12B

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
2.5 40.47 97.7 0.069 -- -- 3.5 32607 31857 0.0 0.0 43.51
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)
2.5 2.59 92.7 0.463 -- 3.2 3.3 3218

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 2.5 40.469 -- 1.42 32607 30530 1514 93.32 0.20657 0.2044 0.2021 0.2477 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 2.5003 2.581 -- 118 2249 0.2469 0.3243 -- 80.0
X Ray Diffraction 2.581 2.6732 -- 124 2432 0.2325 0.2971 -- 87.0
X Ray Diffraction 2.6732 2.7802 -- 128 2533 0.2409 0.3018 -- 90.0
X Ray Diffraction 2.7802 2.9067 -- 136 2612 0.2475 0.3344 -- 93.0
X Ray Diffraction 2.9067 3.0599 -- 139 2674 0.2301 0.3109 -- 95.0
X Ray Diffraction 3.0599 3.2515 -- 138 2694 0.2318 0.2926 -- 96.0
X Ray Diffraction 3.2515 3.5025 -- 147 2744 0.2162 0.2586 -- 97.0
X Ray Diffraction 3.5025 3.8547 -- 143 2710 0.2222 0.2798 -- 96.0
X Ray Diffraction 3.8547 4.4119 -- 142 2724 0.1726 0.2074 -- 96.0
X Ray Diffraction 4.4119 5.5562 -- 149 2814 0.1596 0.1851 -- 99.0
X Ray Diffraction 5.5562 40.4746 -- 150 2830 0.1871 0.212 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic/TLS
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.042
f_dihedral_angle_d 11.815
f_angle_d 0.549
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6398
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 153

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHASER model building
CBASS data collection