X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details 25% PEG 3350, 0.1M BIS-TRIS, 0.2M MAGNESIUM SULFATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.31 α = 90
b = 89.31 β = 90
c = 104.19 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION (WITH 2:1 HORIZONTAL DEMAGNIFICATION) 2010-05-24
Diffraction Radiation
Monochromator Protocol
BARTELS MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA

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
1.73 50 99.8 0.13 -- -- 10.271 84445 n/a -3.0 -3.0 --
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)
1.73 1.83 98.6 0.853 -- 2.9 10.0 --

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
SIRAS 1.73 30.0 -- 0.0 44675 42440 2235 100.0 0.17905 0.17905 0.177 0.21819 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 1.73 1.773 3020 159 3020 0.199 0.249 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.147
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.208
r_scbond_it 2.196
r_nbd_refined 0.207
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.09
r_dihedral_angle_4_deg 8.109
r_dihedral_angle_3_deg 11.893
r_dihedral_angle_2_deg 37.355
r_dihedral_angle_1_deg 6.106
r_angle_other_deg 0.932
r_angle_refined_deg 1.399
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_nbd_other 0.193
r_nbtor_refined 0.171
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.147
r_metal_ion_refined 0.039
r_symmetry_vdw_refined 0.269
r_symmetry_vdw_other 0.261
r_symmetry_hbond_refined 0.206
r_symmetry_hbond_other 0.113
r_mcbond_it 0.921
r_mcbond_other 0.221
r_mcangle_it 1.246
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3088
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 391

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
SHARP model building
MAR345dtb data collection