X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details PEG 3350, MES, MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.64 α = 90
b = 108.64 β = 90
c = 74.75 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 toroidal mirror 2001-06-21
Diffraction Radiation
Monochromator Protocol
Channel-Cut Si(111)Monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.97827, 0.978423, 0.95 NSLS X12C

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
3.1 47.14 95.0 0.066 -- -- 11.2 5054 4796 1.0 1.0 --
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)
3.1 3.21 97.2 0.303 -- 9.2 5.6 --

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
MAD 3.1 47.14 -- 1.0 5054 4290 501 100.0 0.27254 0.27254 0.27074 0.28797 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 3.1 3.184 -- 44 277 0.347 0.345 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.993
Anisotropic B[1][1] 2.18
Anisotropic B[1][2] 1.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.26
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.263
r_gen_planes_refined 0.004
r_chiral_restr 0.073
r_dihedral_angle_1_deg 4.448
r_angle_refined_deg 1.184
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.126
r_symmetry_vdw_refined 0.207
r_symmetry_hbond_refined 0.114
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 592
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement