X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details PEG 8000, magnesium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.48 α = 90
b = 97.23 β = 97.09
c = 69.88 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-03-23
Diffraction Radiation
Monochromator Protocol
double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.282, 1.283, 1.240, 1.333 SSRL BL9-2

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 94.9 0.035 -- -- 3.8 54629 51843 0.0 0.0 --
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)
1.95 2.02 94.1 0.334 -- 2.98 3.4 5106

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
MAD 2.0 20.0 -- 0.0 45667 45667 2432 96.82 0.24637 0.24637 0.24473 0.27727 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 2.0 2.051 3420 179 3420 0.274 0.261 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.52
Anisotropic B[1][1] 2.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.01
Anisotropic B[2][2] -2.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.03
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.006
r_angle_refined_deg 0.848
r_scbond_it 1.25
r_symmetry_vdw_refined 0.136
r_symmetry_hbond_refined 0.036
r_nbd_refined 0.161
r_xyhbond_nbd_refined 0.094
r_mcbond_it 0.469
r_scangle_it 1.92
r_gen_planes_refined 0.002
r_dihedral_angle_1_deg 4.501
r_mcangle_it 0.886
r_chiral_restr 0.056
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5196
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 176

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing