X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 293.0
Details 2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.97 α = 90
b = 134.04 β = 90
c = 54.42 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2008-08-02
Diffraction Radiation
Monochromator Protocol
cryogenically cooled 220 silicon monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C

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
2.35 50 99.7 -- 0.071 -- 6.9 22014 22014 1.0 1.0 43.2
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)
2.35 2.39 96.5 -- 0.497 2.8 5.2 1039

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 2.35 48.402 -- 1.34 -- 21942 1128 99.6 -- 0.2088 0.2075 0.2337 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 2.35 2.457 -- 141 2487 0.2756 0.3133 -- 97.0
X Ray Diffraction 2.457 2.5866 -- 131 2602 0.2388 0.2963 -- 100.0
X Ray Diffraction 2.5866 2.7486 -- 134 2549 0.233 0.2567 -- 100.0
X Ray Diffraction 2.7486 2.9608 -- 151 2564 0.2211 0.2677 -- 100.0
X Ray Diffraction 2.9608 3.2587 -- 142 2576 0.213 0.2359 -- 100.0
X Ray Diffraction 3.2587 3.7301 -- 139 2622 0.1769 0.2144 -- 100.0
X Ray Diffraction 3.7301 4.6989 -- 138 2651 0.163 0.177 -- 100.0
X Ray Diffraction 4.6989 48.4123 -- 152 2763 0.2192 0.2351 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -10.4501
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 12.1077
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6576
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 22.599
f_plane_restr 0.004
f_angle_d 0.949
f_bond_d 0.005
f_chiral_restr 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3250
Nucleic Acid Atoms 0
Heterogen Atoms 160
Solvent Atoms 165

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
PHENIX refinement version: (phenix.refine)
HKL-2000 data reduction
HKL-2000 data scaling