X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 295.0
Details 1.6M Ammonium sulphate, Tri-Na citrate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.13 α = 90
b = 62.13 β = 90
c = 111 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 mirrors 2008-10-08
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.0000 PAL/PLS 6C1

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
1.85 30 93.38 0.06 0.25 -- 12.0 17907 16979 0.0 0.0 35.0
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)
1.85 1.92 52.0 0.06 0.25 2.4 3.3 963

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 1.85 30.0 -- -- 17907 16979 911 93.38 0.20561 0.20561 0.20375 0.24171 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 1.853 1.901 -- 40 611 0.273 0.334 -- 47.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.063
Anisotropic B[1][1] 1.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.04
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.247
r_scbond_it 2.75
r_symmetry_hbond_refined 0.135
r_dihedral_angle_4_deg 18.872
r_gen_planes_refined 0.007
r_dihedral_angle_1_deg 5.679
r_dihedral_angle_3_deg 18.203
r_xyhbond_nbd_refined 0.196
r_angle_refined_deg 1.38
r_nbtor_refined 0.313
r_scangle_it 4.389
r_mcangle_it 1.785
r_symmetry_metal_ion_refined 0.291
r_mcbond_it 0.935
r_bond_refined_d 0.014
r_dihedral_angle_2_deg 34.997
r_chiral_restr 0.104
r_symmetry_vdw_refined 0.274
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1146
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 91

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling