X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 100 mM sodium cacodylate, 200 mM calcium acetate, 18% PEG-8000, 4 mM MgCl2, 50 uM UTP, crystals soaked in 10 mM UMP for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.62 α = 90
b = 41.92 β = 94.37
c = 106.02 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2006-07-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 0.979 SSRL BL1-5

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
2.4 41.92 93.8 0.14 -- -- 3.38 -- 26495 -- -- --
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)
2.4 2.49 93.0 0.476 -- 2.3 3.48 2610

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 2.4 38.98 -- 0.0 -- 26486 1364 93.8 -- 0.226 0.223 0.293 test set taken from 2IKF
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 2.4 2.462 1949 101 1848 0.289 0.362 -- 92.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.465
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.004
r_dihedral_angle_4_deg 19.765
r_dihedral_angle_2_deg 35.658
r_chiral_restr 0.096
r_nbtor_refined 0.309
r_symmetry_vdw_refined 0.234
r_bond_refined_d 0.012
r_xyhbond_nbd_refined 0.171
r_mcbond_it 0.654
r_symmetry_hbond_refined 0.133
r_mcangle_it 1.151
r_scangle_it 2.301
r_nbd_refined 0.224
r_dihedral_angle_1_deg 6.096
r_gen_planes_refined 0.005
r_angle_refined_deg 1.553
r_scbond_it 1.436
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5132
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 184

Software

Software
Software Name Purpose
d*TREK data scaling version: 9.2L
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 2.000
Blu-Ice data collection version: Ice
d*TREK data reduction
PHASER phasing