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_dihedral_angle_1_deg 6.728
r_nbd_refined 0.201
r_mcbond_it 1.104
r_mcangle_it 2.022
r_bond_refined_d 0.015
r_scbond_it 2.858
r_symmetry_hbond_refined 0.095
r_xyhbond_nbd_refined 0.133
r_angle_refined_deg 1.599
r_chiral_restr 0.123
r_gen_planes_refined 0.007
r_scangle_it 4.633
r_symmetry_vdw_refined 0.26
r_dihedral_angle_2_deg 12.298
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.09 Structure Refinement
Software
Software Name Purpose
AMoRE model building
SCALEPACK data reduction
REFMAC version: 5.1.09 refinement
DENZO data collection