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 = 99.08 α = 90
b = 99.08 β = 90
c = 290.29 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 mirrors 2001-09-23
Diffraction Radiation
Monochromator Protocol
Double crystal,Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4

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
2.99 40 99.6 0.114 0.114 -- 14.3 30043 30043 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)
2.99 3.05 100.0 0.42 0.42 6.6 -- --

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
MOLECULAR REPLACEMENT 2.99 19.96 0.0 0.0 28433 28433 1518 19.96 0.2187 0.21878 0.21754 0.24297 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 2.99 3.071 -- 109 2019 0.299 0.325 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.633
Anisotropic B[1][1] -1.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.08
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.061
r_nbd_other 0.251
r_nbd_refined 0.273
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.094
r_dihedral_angle_2_deg 19.818
r_dihedral_angle_1_deg 3.82
r_angle_other_deg 0.884
r_angle_refined_deg 1.77
r_bond_other_d 0.001
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.148
r_xyhbond_nbd_other 0.111
r_symmetry_vdw_refined 0.221
r_symmetry_vdw_other 0.332
r_symmetry_hbond_refined 0.143
r_mcbond_it 0.673
r_mcangle_it 1.279
r_scbond_it 1.232
r_scangle_it 2.303
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5447
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)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement