X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 288.0
Details sodium malonate, magnesium chloride, DTT, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.99 α = 90
b = 98.99 β = 90
c = 291.49 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 ADSC QUANTUM 4 Mirror 2001-12-07
Diffraction Radiation
Monochromator Protocol
Diamond(111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
3.2 43 100.0 0.12 0.12 -- 11.1 24829 24829 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)
3.2 3.31 100.0 0.38 0.38 5.2 11.44 --

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
MOLECULAR REPLACEMENT 3.2 43.0 0.0 0.0 23498 23498 1261 99.74 0.2061 0.2061 0.20376 0.251 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 3.2 3.283 -- 94 1672 0.233 0.327 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.666
Anisotropic B[1][1] -0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.63
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.006
r_nbd_other 0.283
r_nbd_refined 0.319
r_gen_planes_other 0.003
r_gen_planes_refined 0.007
r_chiral_restr 0.134
r_dihedral_angle_2_deg 22.742
r_dihedral_angle_1_deg 4.59
r_angle_other_deg 1.024
r_angle_refined_deg 2.048
r_bond_other_d 0.002
r_bond_refined_d 0.023
r_xyhbond_nbd_refined 0.202
r_xyhbond_nbd_other 0.172
r_symmetry_vdw_refined 0.202
r_symmetry_vdw_other 0.278
r_symmetry_hbond_refined 0.26
r_symmetry_hbond_other 0.077
r_mcbond_it 0.905
r_mcangle_it 1.736
r_scbond_it 2.166
r_scangle_it 3.848
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5528
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 27

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement