X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG 6000, tris-HCl, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.2 α = 90
b = 67.3 β = 90
c = 78.2 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MACSCIENCE -- 1997-02-26
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR571 1.5418 -- --

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
2.1 15 99.3 -- 0.088 -- 5.4 18318 18318 0.0 0.0 22.0
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)
2.1 2.17 99.9 -- 0.403 4.1 5.3 1808

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 2.1 15.0 0.0 0.0 18282 17342 940 99.07 0.1645 0.16453 0.1632 0.18891 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 2.1 2.153 1209 67 1209 0.186 0.253 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 20.71
Anisotropic B[1][1] 0.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.9
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.02
r_scbond_it 2.407
r_mcangle_it 1.651
r_mcbond_it 0.849
r_symmetry_hbond_refined 0.185
r_symmetry_vdw_other 0.224
r_symmetry_vdw_refined 0.158
r_xyhbond_nbd_other 0.029
r_bond_refined_d 0.013
r_bond_other_d 0.001
r_angle_refined_deg 1.406
r_angle_other_deg 0.743
r_dihedral_angle_1_deg 4.07
r_dihedral_angle_3_deg 14.732
r_chiral_restr 0.091
r_gen_planes_refined 0.006
r_gen_planes_other 0.003
r_nbd_refined 0.21
r_nbd_other 0.21
r_xyhbond_nbd_refined 0.154
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2532
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 208

Software

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