X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.9
Temperature 293.15
Details 24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.47 α = 90
b = 54.81 β = 90
c = 92.63 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-03-13
Diffraction Radiation
Monochromator Protocol
Cryogenically-cooled Si(111) double-crystal system SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.00808 APS 17-ID

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 99.4 0.135 -- -- 3.86 14781 14696 0.0 0.0 --
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)
2.0 2.07 100.0 0.421 -- 2.5 3.9 1447

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 2.0 4.99 -- 0.0 14781 14668 745 99.26 0.21938 0.21938 0.21583 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 2.0 2.043 972 54 918 0.217 0.29 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.689
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.077
r_mcbond_it 0.838
r_symmetry_vdw_refined 0.442
r_gen_planes_refined 0.004
r_angle_other_deg 0.795
r_nbd_refined 0.213
r_angle_refined_deg 1.237
r_xyhbond_nbd_refined 0.256
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_symmetry_metal_ion_refined 0.493
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 15.311
r_mcbond_other 0.142
r_dihedral_angle_1_deg 5.667
r_nbd_other 0.179
r_mcangle_it 0.965
r_scbond_it 1.775
r_symmetry_vdw_other 0.202
r_metal_ion_refined 0.243
r_scangle_it 2.746
r_dihedral_angle_3_deg 15.577
r_nbtor_other 0.083
r_nbtor_refined 0.168
r_symmetry_hbond_refined 0.243
r_dihedral_angle_2_deg 41.294
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1840
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 189

Software

Software
Software Name Purpose
d*TREK data scaling version: 9.5LDz
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701
JDirector data collection