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_scangle_it 3.636
r_scbond_it 2.335
r_mcangle_it 1.338
r_mcbond_it 0.946
r_nbd_refined 0.22
r_gen_planes_refined 0.006
r_chiral_restr 0.11
r_dihedral_angle_4_deg 21.553
r_dihedral_angle_3_deg 19.386
r_dihedral_angle_2_deg 32.962
r_dihedral_angle_1_deg 5.925
r_angle_refined_deg 1.592
r_bond_refined_d 0.017
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.174
r_symmetry_vdw_refined 0.258
r_symmetry_hbond_refined 0.228
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

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SOLVE, SHARP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SHARP model building
SOLVE model building
XDS data reduction
MAR data collection