X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 9
Temperature 277.0
Details 2.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.41 α = 90
b = 79.41 β = 90
c = 50.69 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Flat mirror 2004-07-08
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1

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
1.31 23.13 96.3 -- 0.072 -- 5.9 -- 27579 -- -- 22.87
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)
1.31 1.38 85.5 -- 0.654 1.7 1.9 3555

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 1.31 23.13 -- -- -- 26191 1388 96.25 -- 0.15871 0.1574 0.18503 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 1.31 1.344 -- 90 1662 0.289 0.342 -- 82.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.267
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.361
r_symmetry_metal_ion_refined 0.066
r_symmetry_vdw_other 0.167
r_nbd_refined 0.208
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 5.497
r_dihedral_angle_2_deg 41.518
r_chiral_restr 0.097
r_xyhbond_nbd_refined 0.142
r_scangle_it 4.714
r_mcbond_it 1.483
r_nbtor_refined 0.176
r_nbd_other 0.171
r_nbtor_other 0.083
r_bond_other_d 0.001
r_angle_other_deg 0.785
r_symmetry_hbond_refined 0.194
r_dihedral_angle_3_deg 12.187
r_dihedral_angle_4_deg 19.779
r_scbond_it 3.291
r_bond_refined_d 0.013
r_metal_ion_refined 0.062
r_symmetry_vdw_refined 0.36
r_angle_refined_deg 1.339
r_mcbond_other 0.452
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 995
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 159

Software

Software
Software Name Purpose
XDS data scaling
SCALA data scaling version: 5.0)
MOLREP phasing
REFMAC refinement version: (5.2.0005)
XDS data reduction
CCP4 data scaling version: (SCALA)