X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 25% PEG 3350, 0.1M HEPES, 0.2M lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.43 α = 90
b = 89.43 β = 90
c = 104.23 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
1.87 50 99.6 0.1 -- -- 4.28 66642 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)
1.87 1.99 98.0 0.645 -- 2.24 4.18 10559

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 1.87 30.0 -- 0.0 35374 33607 1767 100.0 0.19013 0.19013 0.18769 0.23663 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 1.872 1.921 2367 125 2367 0.212 0.283 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.7
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.522
r_scbond_it 2.376
r_mcangle_it 1.389
r_mcbond_other 0.272
r_mcbond_it 1.018
r_symmetry_hbond_refined 0.166
r_symmetry_vdw_other 0.26
r_symmetry_vdw_refined 0.113
r_xyhbond_nbd_refined 0.162
r_nbtor_other 0.086
r_nbtor_refined 0.171
r_nbd_other 0.199
r_bond_refined_d 0.017
r_bond_other_d 0.002
r_angle_refined_deg 1.601
r_angle_other_deg 1.041
r_dihedral_angle_1_deg 6.428
r_dihedral_angle_2_deg 37.705
r_dihedral_angle_3_deg 12.114
r_dihedral_angle_4_deg 9.183
r_chiral_restr 0.107
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_nbd_refined 0.203
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3074
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 281

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