X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 277.0
Details 25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.53 α = 90
b = 103.12 β = 97.6
c = 77.59 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 315 Mirrors 2008-04-21
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.28130 ESRF ID23-1

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
2.8 20 99.7 0.137 -- -- 7.2 18343 18284 -- -3.0 25.535
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)
2.8 2.9 99.7 0.746 -- 3.88 6.84 1802

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 2.8 20.0 -- -- -- 17318 912 100.0 -- 0.20502 0.20237 0.25614 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 2.8 2.871 1243 66 1243 0.274 0.336 0.394 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.535
Anisotropic B[1][1] -2.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.36
Anisotropic B[2][2] 5.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.97
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.419
r_symmetry_vdw_other 0.194
r_metal_ion_refined 0.061
r_symmetry_vdw_refined 0.197
r_mcangle_it 0.665
r_nbd_refined 0.22
r_scbond_it 1.219
r_dihedral_angle_1_deg 5.762
r_mcbond_other 0.11
r_scangle_it 1.684
r_angle_other_deg 1.062
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 34.953
r_dihedral_angle_3_deg 17.741
r_bond_other_d 0.018
r_nbtor_refined 0.182
r_bond_refined_d 0.016
r_mcbond_it 0.675
r_nbtor_other 0.09
r_xyhbond_nbd_refined 0.138
r_nbd_other 0.181
r_chiral_restr 0.087
r_dihedral_angle_4_deg 9.05
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5043
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 4

Software

Software
Software Name Purpose
REFMAC refinement version: 5.3.0040
ADSC data collection version: Quantum
XDS data reduction
XSCALE data scaling
PHASER phasing