X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 292.0
Details Sodium malonate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.46 α = 90
b = 70.46 β = 90
c = 215.3 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Rh coated silicon mirror 2002-11-24
Diffraction Radiation
Monochromator Protocol
slits SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX14.2 0.978 SRS PX14.2

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
1.29 60 99.0 -- 0.097 -- 52.5 4278064 81391 0.0 2.0 15.3
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)
1.29 1.3 97.9 -- 0.77 4.4 -- --

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 1.29 58.71 -- -- 81391 76434 4045 98.93 0.1533 0.1533 0.1526 0.16637 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 1.285 1.318 -- 278 5376 0.237 0.251 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 7.724
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.16
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.011
r_gen_planes_other 0.003
r_angle_refined_deg 1.33
r_nbtor_other 0.112
r_nbd_other 0.248
r_dihedral_angle_1_deg 6.368
r_angle_other_deg 0.84
r_chiral_restr 0.089
r_xyhbond_nbd_refined 0.233
r_nbd_refined 0.217
r_symmetry_vdw_other 0.303
r_symmetry_hbond_refined 0.261
r_scbond_it 1.307
r_symmetry_vdw_refined 0.235
r_mcangle_it 0.822
r_bond_other_d 0.002
r_gen_planes_refined 0.005
r_scangle_it 1.962
r_mcbond_it 0.477
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1779
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 389

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
CNS phasing