X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 292.0
Details 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.13 α = 90
b = 49.13 β = 102.4
c = 80.5 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2006-03-20
Diffraction Radiation
Monochromator Protocol
Bent Si (111) crystal, horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.04300 MAX II I911-2

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
1.4 30 100.0 0.071 -- -- 4.5 110982 110982 -- -3.0 27.1
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)
1.4 1.45 100.0 0.49 -- 2.7 3.1 11024

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 1.4 20.0 -- -- 109834 109834 1117 99.66 0.16153 0.16153 0.16128 0.1859 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 1.401 1.437 7675 96 7675 0.225 0.236 -- 95.64
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic model of ADP parameters
Mean Isotropic B 16.815
Anisotropic B[1][1] -1.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.24
Anisotropic B[2][2] -1.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.93
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 6.286
r_sphericity_free 10.357
r_rigid_bond_restr 1.706
r_scangle_it 5.136
r_scbond_it 3.625
r_nbd_refined 0.219
r_gen_planes_other 0.001
r_gen_planes_refined 0.009
r_chiral_restr 0.123
r_dihedral_angle_4_deg 17.295
r_dihedral_angle_3_deg 12.074
r_dihedral_angle_2_deg 32.631
r_dihedral_angle_1_deg 6.271
r_angle_other_deg 0.935
r_angle_refined_deg 1.731
r_bond_other_d 0.001
r_bond_refined_d 0.019
r_nbd_other 0.171
r_nbtor_refined 0.182
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.113
r_metal_ion_refined 0.096
r_symmetry_vdw_refined 0.151
r_symmetry_vdw_other 0.223
r_symmetry_hbond_refined 0.161
r_symmetry_metal_ion_refined 0.048
r_mcbond_it 1.897
r_mcbond_other 1.104
r_mcangle_it 2.691
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5046
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 506

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement
MOLREP model building
MAR345dtb data collection