X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 293.15
Details VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.75 α = 90
b = 63.64 β = 110.45
c = 74.71 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 ADSC QUANTUM 4 -- 2002-06-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 1.100 NSLS X8C

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
1.6 70 94.5 -- 0.088 -- 16.18 -- 53851 0.0 -3.0 15.3
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)
1.6 1.642 93.4 0.32 0.32 6.35 14.28 5643

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 1.6 70.0 -- -- -- 53851 2896 94.46 -- 0.19577 0.19377 0.23208 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 1.6 1.642 -- 215 4063 0.159 0.25 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.669
Anisotropic B[1][1] 1.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.82
Anisotropic B[2][2] -1.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.48
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.124
r_xyhbond_nbd_refined 0.213
r_nbd_other 0.247
r_rigid_bond_restr 1.522
r_nbd_refined 0.231
r_sphericity_free 3.671
r_mcbond_it 1.312
r_angle_other_deg 0.903
r_gen_planes_other 0.011
r_scbond_it 2.616
r_gen_planes_refined 0.01
r_bond_other_d 0.002
r_symmetry_hbond_refined 0.206
r_angle_refined_deg 1.623
r_mcangle_it 1.91
r_nbtor_other 0.087
r_scangle_it 3.693
r_dihedral_angle_1_deg 6.88
r_symmetry_vdw_other 0.297
r_bond_refined_d 0.016
r_chiral_restr 0.107
r_symmetry_vdw_refined 0.177
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3128
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 565

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
EPMR phasing