X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.2M Sodium tartrate, 0.1M MOPS, 8% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.83 α = 90
b = 57.83 β = 90
c = 161.62 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2000 -- 2000-05-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS 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
2.5 40.4 99.2 0.094 0.088 -- 7.3 9732 9710 2.367 1.8 56.26
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)
2.5 2.67 94.4 0.455 0.419 4.0 6.3 1298

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 2.5 54.23 1.8 2.36 9710 9166 485 95.17 0.25 0.23326 0.23029 0.28971 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 2.5 2.565 1298 9 240 0.314 0.261 -- 99.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model overall
Mean Isotropic B 30.642
Anisotropic B[1][1] 2.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.7
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.051
r_scbond_it 1.796
r_mcangle_it 1.239
r_nbd_refined 0.278
r_gen_planes_other 0.003
r_gen_planes_refined 0.008
r_chiral_restr 0.103
r_dihedral_angle_3_deg 18.518
r_dihedral_angle_1_deg 5.272
r_angle_other_deg 0.905
r_angle_refined_deg 1.902
r_bond_other_d 0.001
r_bond_refined_d 0.015
r_nbd_other 0.256
r_nbtor_other 0.109
r_xyhbond_nbd_refined 0.152
r_xyhbond_nbd_other 0.253
r_symmetry_vdw_refined 0.241
r_symmetry_vdw_other 0.321
r_symmetry_hbond_refined 0.788
r_symmetry_hbond_other 0.149
r_mcbond_it 0.642
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1490
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 20

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement