X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 300.0
Details 32% PEG 3350, 0.25M MgCl2, 0.1M Na-ascorbate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.76 α = 90
b = 74.76 β = 90
c = 31.38 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-05-13
Diffraction Radiation
Monochromator Protocol
FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 0.991 MAX_II I711

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 19.28 91.0 0.079 -- -- 10.8 6938 6400 -3.0 2.0 26.7
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)
2.0 2.1 91.6 0.298 -- 7.06 7.6 860

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 2.0 19.28 -- -3.0 6244 6244 692 99.34 0.1881 0.1881 0.18322 0.23232 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 2.0 2.055 433 43 433 0.216 0.327 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.337
Anisotropic B[1][1] -1.23
Anisotropic B[1][2] -0.62
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.85
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.187
r_nbd_other 0.245
r_nbtor_other 0.091
r_bond_refined_d 0.019
r_chiral_restr 0.088
r_nbd_refined 0.207
r_gen_planes_other 0.005
r_dihedral_angle_1_deg 5.994
r_scangle_it 4.694
r_gen_planes_refined 0.007
r_scbond_it 2.824
r_angle_refined_deg 1.693
r_symmetry_vdw_other 0.289
r_symmetry_vdw_refined 0.306
r_bond_other_d 0.002
r_angle_other_deg 0.786
r_symmetry_hbond_refined 0.133
r_mcbond_it 1.158
r_mcangle_it 2.017
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.115
Luzzati ESD (R-Free Set) 0.171
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 738
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 40

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
XDS data reduction
XSCALE data scaling