2OZ3 | pdb_00002oz3

Crystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSH	PDB ENTRY 2GSH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	60% Tacsimate, pH 7.0, 10% Glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.772	α = 90
b = 115.397	β = 96.06
c = 164.113	γ = 90

Symmetry
Space Group	C 1 2 1

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	MAR CCD 165 mm	MIRRORS	2006-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97960	APS	31-ID

Data Collection

Overall
ID #	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	2	50	98.1	0.094	0.066	3.7	2.1	412398	412398		-5	31.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	94		0.67	0.56	0.6	1.9	39577

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 2GSH	2	20	200140	200140	6225	96.91	0.1974	0.1974	0.19556	0.2	0.25702	0.26	RANDOM	38.776

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]
-2.05		-1.28	2.03		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.202
r_dihedral_angle_4_deg	21.413
r_dihedral_angle_3_deg	19.231
r_scangle_it	11.201
r_scbond_it	9.139
r_dihedral_angle_1_deg	8.865
r_mcangle_it	6.74
r_mcbond_it	5.331
r_angle_refined_deg	1.195
r_nbtor_refined	0.298
r_symmetry_hbond_refined	0.184
r_metal_ion_refined	0.169
r_xyhbond_nbd_refined	0.165
r_nbd_refined	0.14
r_chiral_restr	0.107
r_symmetry_vdw_refined	0.099
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24735
Nucleic Acid Atoms
Solvent Atoms	1476
Heterogen Atoms	188

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing