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 = 56.96 α = 90
b = 56.96 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
IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRROR 2002-09-05
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.7 50 97.5 -- 0.03 -- 7.2 -- 17163 1.0 -3.0 26.838
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 90.3 -- 0.263 5.1 3.4 1557

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 1.7 49.39 -- 0.0 17150 16284 866 97.64 -- 0.18476 0.18362 0.20573 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 1.7 1.744 1067 59 1067 0.301 0.319 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 20.827
Anisotropic B[1][1] 0.29
Anisotropic B[1][2] 0.15
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.44
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.097
r_nbd_refined 0.214
r_symmetry_vdw_refined 0.195
r_angle_refined_deg 1.725
r_mcangle_it 1.799
r_gen_planes_refined 0.009
r_symmetry_hbond_refined 0.168
r_chiral_restr 0.117
r_xyhbond_nbd_refined 0.153
r_mcbond_it 1.002
r_scbond_it 2.536
r_bond_refined_d 0.016
r_scangle_it 4.104
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 118

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
SOLVE phasing
REFMAC refinement version: 5.1.27
HKL-2000 data reduction
MOLREP phasing