X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 298.0
Details 0.3 M Na Cacodylate 17% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65 α = 90
b = 78.38 β = 90
c = 109.25 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER PROTEUM-R MONTEL OPTICS 2006-07-01
Diffraction Radiation
Monochromator Protocol
GRADED MULTILAYER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 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
1.75 63.63 98.6 -- -- -- -- -- 59622 -- -- --
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)
1.75 1.8 83.5 -- -- -- 4.0 --

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
-- 1.75 63.63 -- 0.0 -- 56091 2878 98.42 0.18 0.18 0.177 0.225 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 1.75 1.795 -- 171 3291 0.275 0.304 -- 83.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.193
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.031
r_symmetry_vdw_refined 0.209
r_scangle_it 2.924
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.152
r_angle_refined_deg 1.38
r_mcangle_it 1.235
r_chiral_restr 0.107
r_symmetry_hbond_refined 0.152
r_scbond_it 1.995
r_dihedral_angle_1_deg 4.917
r_nbd_refined 0.218
r_metal_ion_refined 0.107
r_dihedral_angle_4_deg 14.843
r_gen_planes_refined 0.006
r_nbtor_refined 0.304
r_dihedral_angle_2_deg 36.906
r_mcbond_it 0.829
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4386
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 617

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.000
SAINT data reduction
SCALEPACK data scaling