X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details Crystallization assays were performed in 24 well plates at 25 C using the vapor diffusion, hanging drop method. Best-diffracting crystals obtained from 7 mg/ml protein concentration in 2 M NaK phosphate pH 6.5 with 3% MPD, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.59 α = 90
b = 90.57 β = 90
c = 137.37 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-08-26
Diffraction Radiation
Monochromator Protocol
Silicon 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2

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 40.86 100.0 -- -- -- -- 32975 32975 0.0 0.0 21.76

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 2.1 39.043 -- 0.0 32908 32908 1671 96.58 0.1898 0.1898 0.1872 0.2391 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 2.1 2.1618 -- 123 2610 0.2261 0.2927 -- 97.0
X Ray Diffraction 2.1618 2.2316 -- 147 2522 0.2244 0.3068 -- 97.0
X Ray Diffraction 2.2316 2.3113 -- 145 2561 0.2432 0.2731 -- 97.0
X Ray Diffraction 2.3113 2.4038 -- 120 2619 0.2222 0.2937 -- 97.0
X Ray Diffraction 2.4038 2.5132 -- 138 2572 0.2113 0.2726 -- 97.0
X Ray Diffraction 2.5132 2.6457 -- 147 2556 0.2016 0.2745 -- 97.0
X Ray Diffraction 2.6457 2.8114 -- 143 2582 0.2007 0.2835 -- 97.0
X Ray Diffraction 2.8114 3.0284 -- 141 2574 0.1887 0.2576 -- 96.0
X Ray Diffraction 3.0284 3.333 -- 130 2562 0.1661 0.2199 -- 95.0
X Ray Diffraction 3.333 3.815 -- 140 2592 0.1651 0.202 -- 95.0
X Ray Diffraction 3.815 4.8051 -- 151 2602 0.1403 0.1642 -- 95.0
X Ray Diffraction 4.8051 39.0493 -- 146 2885 0.196 0.2542 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.2119
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.4251
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.637
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_plane_restr 0.004
f_angle_d 1.065
f_chiral_restr 0.072
f_dihedral_angle_d 14.154
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3128
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 418

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.1_743)
MOSFLM data reduction
SCALA data scaling