X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 20mg/ml of protein in 25mM HEPES, pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.85 α = 90
b = 67.85 β = 90
c = 102.48 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2007-02-07
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1

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
1.8 56.61 99.2 0.099 0.099 -- 4.7 -- 22616 -- -- --
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)
1.8 1.9 98.0 0.457 0.457 1.6 4.4 3193

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 1.8 35.02 -- 0.0 -- 22598 1156 98.82 -- 0.184 0.182 0.218 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 1.8 1.847 -- 104 1481 0.216 0.307 -- 96.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.691
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.401
r_dihedral_angle_4_deg 17.183
r_symmetry_vdw_refined 0.416
r_chiral_restr 0.093
r_dihedral_angle_2_deg 38.502
r_scbond_it 1.726
r_nbtor_refined 0.315
r_nbd_refined 0.226
r_symmetry_hbond_refined 0.451
r_dihedral_angle_1_deg 5.685
r_metal_ion_refined 0.161
r_angle_refined_deg 1.358
r_mcbond_it 1.218
r_mcangle_it 1.941
r_xyhbond_nbd_refined 0.21
r_gen_planes_refined 0.006
r_bond_refined_d 0.012
r_dihedral_angle_3_deg 13.858
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2021
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 198

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.25
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum