8G22 | pdb_00008g22

Crystal Structure of the dTDP-4-dehydrorhamnose Reductase from Streptococcus pneumoniae.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 3.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PEG's II (H1), 0.01M tri-Sodium citrate, 33% (w/v) PEG6000;

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.178	α = 90
b = 120.178	β = 90
c = 48.075	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2021-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.77482	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1	30	99.1	0.07	0.07	0.074	0.025	0.997	28	8		138569		-3	17.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.02	98.3		1.207	1.207	0.456	0.502	1.9	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1	22.72	131576	6992	99.06	0.12632	0.12543	0.13	0.14319	0.15	RANDOM	12.486

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]
0.27	0.13		0.27		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	9.825
r_dihedral_angle_1_deg	5.13
r_rigid_bond_restr	4.999
r_dihedral_angle_2_deg	3.506
r_long_range_B_refined	3.265
r_long_range_B_other	2.151
r_scangle_other	1.182
r_angle_refined_deg	1.146
r_mcangle_it	1.077
r_mcangle_other	1.077
r_scbond_it	0.812
r_scbond_other	0.811
r_mcbond_it	0.69
r_mcbond_other	0.69
r_angle_other_deg	0.373
r_chiral_restr	0.058
r_gen_planes_refined	0.015
r_gen_planes_other	0.013
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2299
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing