3DUV | pdb_00003duv

Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the-configuration

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	297	100mM sodium citrate (pH5.6), 50mM ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.418	α = 90
b = 82.609	β = 90
c = 115.712	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6B	0.9792	PAL/PLS	6B

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	2.2	30	93.9	0.051				24031

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)
	2.2	2.28	86.6		0.133

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		THROUGHOUT	2.3	30	20235	2050	95.01	0.177	0.17	0.184	0.236	0.2549	RANDOM	28.969

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]
-1.8			2.97		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.188
r_dihedral_angle_3_deg	18.708
r_dihedral_angle_4_deg	17.976
r_dihedral_angle_1_deg	6.908
r_scangle_it	5.191
r_scbond_it	3.402
r_mcangle_it	2.128
r_angle_refined_deg	2.121
r_mcbond_it	1.397
r_symmetry_hbond_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.188
r_dihedral_angle_3_deg	18.708
r_dihedral_angle_4_deg	17.976
r_dihedral_angle_1_deg	6.908
r_scangle_it	5.191
r_scbond_it	3.402
r_mcangle_it	2.128
r_angle_refined_deg	2.121
r_mcbond_it	1.397
r_symmetry_hbond_refined	0.32
r_nbtor_refined	0.314
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.234
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.168
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3864
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.