2PNK | pdb_00002pnk

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5S	PDB entry 1J5S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.33	277	NANODROP, 7.5% PEG 8000, 36.0% 2-methyl-2,4-pentanediol, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 273.72	α = 90
b = 158.56	β = 116.03
c = 181.24	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-02-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97935	SSRL	BL11-1

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	48.564	93.7	0.072	9.33	2.83		437594			25.43

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)
1	2	2.11	72.2		0.442	2.39	2.58	45786

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 (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, MAD	THROUGHOUT	PDB entry 1J5S	2	48.564	437582	5300	97.54	0.149	0.149	0.148	0.17	0.178	0.25	THIN SHELLS	20.506

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]
0.41		-0.89	1.16		-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.084
r_dihedral_angle_4_deg	16.81
r_dihedral_angle_3_deg	13.025
r_scangle_it	6.513
r_dihedral_angle_1_deg	6.215
r_scbond_it	4.786
r_mcangle_it	2.382
r_angle_refined_deg	1.388
r_mcbond_it	1.33
r_angle_other_deg	0.955
r_mcbond_other	0.495
r_symmetry_vdw_other	0.301
r_nbd_refined	0.214
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.156
r_symmetry_vdw_refined	0.101
r_metal_ion_refined	0.091
r_chiral_restr	0.088
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41334
Nucleic Acid Atoms
Solvent Atoms	3732
Heterogen Atoms	327

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
MOLREP	phasing
SHELXD	phasing
autoSHARP	phasing