X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details 126mM sodium phosphate pH 6.2, 63mM sodium citrate, 27% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.78 α = 90
b = 58.31 β = 90
c = 61.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2006-02-17
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
1.95 50 95.3 0.047 0.047 -- 4.9 -- 13238 0.0 0.0 --

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 1.95 42.37 -- 0.0 -- 12549 664 95.39 -- 0.16828 0.1658 0.21588 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 1.95 2.0 -- 39 914 0.191 0.234 -- 96.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.944
Anisotropic B[1][1] -0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.8
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_bond_refined_d 0.008
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.973
r_symmetry_vdw_other 0.18
r_nbtor_other 0.083
r_scangle_it 2.269
r_dihedral_angle_4_deg 15.218
r_dihedral_angle_2_deg 40.544
r_scbond_it 1.623
r_chiral_restr 0.08
r_symmetry_hbond_refined 0.117
r_angle_refined_deg 1.294
r_dihedral_angle_3_deg 10.692
r_nbd_refined 0.186
r_mcangle_it 1.088
r_symmetry_vdw_refined 0.137
r_mcbond_it 0.812
r_angle_other_deg 0.628
r_xyhbond_nbd_refined 0.17
r_nbtor_refined 0.169
r_mcbond_other 0.205
r_nbd_other 0.187
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1494
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 158

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing