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_rigid_bond_restr 1.706
r_bond_refined_d 0.019
r_mcangle_it 2.691
r_symmetry_hbond_refined 0.161
r_scbond_it 3.625
r_mcbond_it 1.897
r_dihedral_angle_2_deg 32.631
r_dihedral_angle_4_deg 17.295
r_dihedral_angle_3_deg 12.074
r_gen_planes_other 0.001
r_xyhbond_nbd_refined 0.113
r_symmetry_vdw_other 0.223
r_metal_ion_refined 0.096
r_dihedral_angle_1_deg 6.271
r_mcbond_other 1.104
r_sphericity_free 10.357
r_angle_refined_deg 1.731
r_nbtor_other 0.085
r_bond_other_d 0.001
r_scangle_it 5.136
r_sphericity_bonded 6.286
r_chiral_restr 0.123
r_nbd_refined 0.219
r_symmetry_vdw_refined 0.151
r_nbtor_refined 0.182
r_symmetry_metal_ion_refined 0.048
r_nbd_other 0.171
r_gen_planes_refined 0.009
r_angle_other_deg 0.935
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

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
REFMAC refinement version: 5.2.0003
DENZO data reduction
SCALEPACK data scaling