X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details NA cadodalyte, Mg acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.1 α = 90
b = 57.1 β = 90
c = 82.5 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE MIRROR 2002-08-25
Diffraction Radiation
Monochromator Protocol
ROSENBAUM-ROCK DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 1.0080 APS 19-BM

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
1.7 50 95.9 -- 0.036 -- 12.47 -- 17010 -- -3.0 20.32
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)
1.7 1.76 83.2 -- 0.2 4.3 -- --

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 1.7 49.39 -- 0.0 -- 15843 861 94.36 -- 0.186 0.184 0.221 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 1.698 1.742 -- 74 895 0.214 0.243 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.5
Anisotropic B[1][1] -0.21
Anisotropic B[1][2] -0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.227
r_gen_planes_refined 0.008
r_chiral_restr 0.12
r_dihedral_angle_1_deg 6.017
r_angle_refined_deg 1.611
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.158
r_symmetry_vdw_refined 0.18
r_symmetry_hbond_refined 0.158
r_mcbond_it 1.042
r_mcangle_it 1.907
r_scbond_it 2.511
r_scangle_it 3.779
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 130

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.27 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.27 refinement
SOLVE model building
SCALEPACK data reduction
HKL-2000 data collection