X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Microgravity
pH 4.5
Temperature 295.0
Details PEG 6000, sodium chloride, O1-methyl-alpha-D-mannose, acetate buffer, pH 4.5, Vapor diffusion, microgravity, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.45 α = 90
b = 77.96 β = 90
c = 105.32 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirror --
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.38 LNLS D03B-MX1

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
1.77 9.94 99.6 -- 0.068 -- 3.76 25553 25553 -- -- 27.1
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)
1.77 1.81 98.1 -- 0.068 4.9 3.72 1767

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 1.77 9.94 -- 0.0 24265 24265 1288 100.0 0.14173 0.14173 0.14023 0.16991 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 1.77 1.83 -- 124 2256 0.179 0.207 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 11.688
Anisotropic B[1][1] 1.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.98
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.26
r_dihedral_angle_1_deg 6.728
r_bond_refined_d 0.015
r_chiral_restr 0.123
r_mcangle_it 2.022
r_gen_planes_refined 0.007
r_scbond_it 2.858
r_symmetry_hbond_refined 0.095
r_xyhbond_nbd_refined 0.133
r_mcbond_it 1.104
r_dihedral_angle_2_deg 12.298
r_nbd_refined 0.201
r_scangle_it 4.633
r_angle_refined_deg 1.599
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1778
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 179

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.1.09