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_scangle_it 4.694
r_scbond_it 2.824
r_mcangle_it 2.017
r_mcbond_it 1.158
r_symmetry_hbond_refined 0.133
r_symmetry_vdw_other 0.289
r_symmetry_vdw_refined 0.306
r_bond_refined_d 0.019
r_bond_other_d 0.002
r_angle_refined_deg 1.693
r_angle_other_deg 0.786
r_dihedral_angle_1_deg 5.994
r_chiral_restr 0.088
r_gen_planes_refined 0.007
r_gen_planes_other 0.005
r_nbd_refined 0.207
r_nbd_other 0.245
r_nbtor_other 0.091
r_xyhbond_nbd_refined 0.187
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement