3BDK | pdb_00003bdk

Crystal Structure of Streptococcus suis mannonate dehydratase complexed with substrate analogue

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION			EVAPORATION

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.468	α = 90
b = 105.468	β = 90
c = 160.155	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	50		0.063	39.9	13.3		31751

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59			0.509	2.98	8.8	2817

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1vl8	2.5	45.27	28821	1550	95.31	0.25283	0.25016	0.25	0.30287	0.3	RANDOM	44.905

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.66			-0.66		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.131
r_dihedral_angle_4_deg	18.366
r_dihedral_angle_3_deg	18.056
r_dihedral_angle_1_deg	6.657
r_scangle_it	2.023
r_angle_refined_deg	1.45
r_scbond_it	1.306
r_mcangle_it	1.173
r_mcbond_it	0.664
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.131
r_dihedral_angle_4_deg	18.366
r_dihedral_angle_3_deg	18.056
r_dihedral_angle_1_deg	6.657
r_scangle_it	2.023
r_angle_refined_deg	1.45
r_scbond_it	1.306
r_mcangle_it	1.173
r_mcbond_it	0.664
r_nbtor_refined	0.316
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.149
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5471
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.