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 = 98.94 α = 90
b = 98.94 β = 90
c = 289.15 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 -- 2002-07-22
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
3 40 99.8 0.11 0.11 -- 10.35 28924 28924 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)
3.0 3.05 98.4 0.45 0.45 4.1 -- --

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 3.0 40.0 0.0 0.0 28258 28258 1508 99.9 0.2084 0.20847 0.20621 0.2524 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 3.0 3.074 -- 102 1997 0.286 0.396 -- 98.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.085
Anisotropic B[1][1] -0.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.2
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.258
r_nbd_refined 0.305
r_gen_planes_other 0.003
r_gen_planes_refined 0.009
r_chiral_restr 0.135
r_dihedral_angle_2_deg 20.927
r_dihedral_angle_1_deg 5.011
r_angle_other_deg 0.992
r_angle_refined_deg 2.359
r_bond_other_d 0.001
r_bond_refined_d 0.029
r_xyhbond_nbd_refined 0.184
r_xyhbond_nbd_other 0.127
r_metal_ion_refined 0.066
r_symmetry_vdw_refined 0.198
r_symmetry_vdw_other 0.262
r_symmetry_hbond_refined 0.119
r_mcbond_it 1.014
r_mcangle_it 1.945
r_scbond_it 2.798
r_scangle_it 4.91
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5436
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 0

Software

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