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 = 99.14 α = 90
b = 99.14 β = 90
c = 289.54 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 -- 2002-07-21
Diffraction Radiation
Monochromator Protocol
Diamond(111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9393 ESRF ID14-1

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
2.8 40 99.1 0.079 0.079 -- 7.94 36371 36371 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)
2.8 2.85 99.1 0.286 0.286 5.5 -- --

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 2.8 40.0 0.0 0.0 34536 34536 1815 99.26 0.2166 0.2166 0.21507 0.2464 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 2.8 2.871 -- 147 2473 0.283 0.366 -- 99.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.589
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 16.961
r_angle_refined_deg 1.931
r_angle_other_deg 0.926
r_chiral_restr 0.108
r_nbd_other 0.227
r_symmetry_vdw_other 0.234
r_gen_planes_other 0.003
r_symmetry_vdw_refined 0.174
r_nbd_refined 0.271
r_dihedral_angle_1_deg 3.373
r_bond_other_d 0.001
r_xyhbond_nbd_other 0.083
r_scangle_it 4.397
r_bond_refined_d 0.023
r_scbond_it 2.564
r_xyhbond_nbd_refined 0.138
r_symmetry_hbond_refined 0.093
r_mcangle_it 1.92
r_gen_planes_refined 0.008
r_mcbond_it 1.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5423
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 11

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing