X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 289.0
Details 0.1 M PCB buffer, 20 % v/v PEG 1500, 10 mM spermidine , pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.02 α = 90
b = 48.02 β = 90
c = 218.35 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2008-11-06
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.933000 ESRF ID14-4

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
2.4 38.86 95.6 0.048 -- -- -- -- 21045 -- -3.0 59.528
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)
2.4 2.5 85.4 0.542 -- 1.46 -- --

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 2.4 38.86 -- 0.0 21045 21041 1069 95.8 -- 0.2002 0.1972 0.2599 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 2.4 2.462 -- 62 1211 0.292 0.374 -- 82.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.385
Anisotropic B[1][1] 0.42
Anisotropic B[1][2] 0.42
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.37
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.092
r_dihedral_angle_4_deg 19.325
r_dihedral_angle_3_deg 18.365
r_dihedral_angle_2_deg 36.805
r_dihedral_angle_1_deg 5.816
r_angle_other_deg 1.168
r_angle_refined_deg 1.522
r_bond_other_d 0.002
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2458
Nucleic Acid Atoms 2050
Heterogen Atoms 0
Solvent Atoms 23

Software

Computing
Computing Package Purpose
DNA Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.1 molecular replacement
Xscale data reduction