4D4A

Structure of the catalytic domain (BcGH76) of the Bacillus circulans GH76 alpha mannanase, Aman6.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.84 α = 90
b = 85.42 β = 90
c = 102.02 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
PIXEL DECTRIS PILATUS 2M -- 2014-03-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 -- Diamond I04-1

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
1.4 43.8 98.4 0.07 -- -- 8.3 -- 141868 -- -3.7 14.0
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)
1.4 1.42 96.3 1.37 -- 1.7 8.1 --

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 1.4 65.49 -- -- -- 134900 6900 98.12 -- 0.11786 0.116 0.15423 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 1.399 1.436 -- 514 9672 0.245 0.284 -- 96.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.257
Anisotropic B[1][1] 0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.185
r_dihedral_angle_4_deg 22.991
r_nbd_other 0.177
r_symmetry_hbond_refined 0.034
r_bond_other_d 0.001
r_xyhbond_nbd_refined 0.117
r_angle_other_deg 0.84
r_dihedral_angle_1_deg 5.247
r_mcbond_it 1.693
r_xyhbond_nbd_other 0.004
r_symmetry_vdw_refined 0.286
r_scbond_it 2.541
r_gen_planes_refined 0.006
r_nbtor_other 0.076
r_dihedral_angle_3_deg 11.325
r_scangle_it 2.951
r_rigid_bond_restr 1.855
r_nbd_refined 0.256
r_sphericity_free 40.671
r_mcbond_other 1.643
r_sphericity_bonded 12.079
r_angle_refined_deg 1.256
r_chiral_restr 0.08
r_bond_refined_d 0.008
r_dihedral_angle_2_deg 37.21
r_symmetry_vdw_other 0.274
r_mcangle_it 2.092
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5408
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 965

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
XDS data reduction
Aimless data scaling
PHASER phasing