2Z8U

Methanococcus jannaschii TBP


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details PEG MME 2000, sodium acetate, ammonium sulfate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.24 α = 90
b = 55.53 β = 91.05
c = 123.43 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2004-06-10
Diffraction Radiation
Monochromator Protocol
SI111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97910 Photon Factory BL-5A

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
1.9 62 99.9 0.039 -- -- -- 57094 57094 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)
1.9 2.0 99.9 0.35 -- 2.1 -- --

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 1.9 50.0 -- -- -- 54183 2892 100.0 -- 0.22734 0.22557 0.25911 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 1.9 1.949 3944 197 3944 0.274 0.352 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.653
Anisotropic B[1][1] -0.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] 1.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.371
r_angle_refined_deg 1.29
r_symmetry_vdw_refined 0.228
r_dihedral_angle_2_deg 41.592
r_gen_planes_refined 0.005
r_scbond_it 1.826
r_chiral_restr 0.08
r_mcangle_it 1.153
r_mcbond_it 0.729
r_scangle_it 2.948
r_dihedral_angle_4_deg 23.135
r_dihedral_angle_3_deg 16.133
r_bond_refined_d 0.012
r_nbd_refined 0.211
r_symmetry_hbond_refined 0.135
r_xyhbond_nbd_refined 0.137
r_nbtor_refined 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5323
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 277

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MOSFLM data reduction
SCALA data scaling
MOLREP phasing