X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.12 α = 90
b = 126.12 β = 90
c = 76.04 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-11-08
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.937 ESRF ID14-1

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
1.35 64.55 99.6 0.075 0.075 -- 4.6 66690 66690 0.0 0.0 16.2
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)
1.35 1.39 99.7 0.395 0.395 2.3 3.3 4901

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 1.35 19.94 -- 0.0 63280 63280 3366 99.51 0.16227 0.16227 0.1603 0.20049 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 1.35 1.385 -- 244 4637 0.188 0.252 -- 99.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.002
Anisotropic B[1][1] -0.01
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] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.887
r_nbd_refined 0.219
r_nbtor_refined 0.318
r_xyhbond_nbd_refined 0.147
r_rigid_bond_restr 4.083
r_sphericity_free 10.775
r_mcbond_it 4.204
r_symmetry_hbond_refined 0.203
r_mcangle_it 5.117
r_bond_refined_d 0.02
r_scbond_it 6.29
r_dihedral_angle_3_deg 12.231
r_symmetry_vdw_refined 0.248
r_scangle_it 8.041
r_dihedral_angle_2_deg 36.355
r_dihedral_angle_4_deg 18.681
r_sphericity_bonded 8.51
r_chiral_restr 0.143
r_gen_planes_refined 0.012
r_dihedral_angle_1_deg 7.268
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1979
Nucleic Acid Atoms 0
Heterogen Atoms 142
Solvent Atoms 245

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DNA data collection
MOSFLM data reduction
SCALA data scaling
MOLREP phasing