X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details PEG 3350, Na-cacodylate, MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.69 α = 90
b = 89.77 β = 90
c = 189.07 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-02-01
Diffraction Radiation
Monochromator Protocol
Silicon mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.9795 APS 5ID-B

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
2.3 27.7 98.1 -- 0.064 -- 6.7 53175 53175 0.0 0.0 --
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)
2.3 -- 94.8 -- 0.262 2.9 6.0 --

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
SAD 2.3 26.44 -- -- 50430 50430 2687 97.91 -- 0.22046 0.21668 0.29227 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 2.3 2.359 -- 201 3518 0.258 0.368 -- 94.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.487
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.592
r_nbtor_refined 0.307
r_scbond_it 2.335
r_mcangle_it 1.338
r_bond_refined_d 0.017
r_symmetry_hbond_refined 0.228
r_dihedral_angle_3_deg 19.386
r_mcbond_it 0.946
r_xyhbond_nbd_refined 0.174
r_dihedral_angle_1_deg 5.925
r_symmetry_vdw_refined 0.258
r_dihedral_angle_2_deg 32.962
r_nbd_refined 0.22
r_chiral_restr 0.11
r_dihedral_angle_4_deg 21.553
r_scangle_it 3.636
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8410
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 516

Software

Software
Software Name Purpose
MAR345 data collection
XDS data reduction
SOLVE phasing
SHARP phasing
REFMAC refinement version: 5.0
XDS data scaling