1XRT | pdb_00001xrt

The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex Aeolicus at 1.7 A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	ethanol, peg 400, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.75	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.201	α = 90
b = 91.235	β = 93.15
c = 61.183	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	93	IMAGE PLATE	RIGAKU RAXIS HTC	OSMIC MIRRORS	2002-02-28	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.609	20	79.2	0.105	4.8	6.5	121022	95834

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.609	1.67	14.5		0.243	2.8	3	1466

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 1XRF	1.609	20	121022	90961	4873	77.56	0.1669	0.16688	0.16463	0.17	0.20794	0.21	RANDOM	18.931

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]
-2.52		0.12	-0.81		3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.148
r_scangle_it	5.431
r_scbond_it	3.192
r_mcangle_it	1.907
r_angle_refined_deg	1.77
r_mcbond_it	1.102
r_angle_other_deg	0.925
r_nbd_other	0.254
r_symmetry_vdw_refined	0.254
r_symmetry_vdw_other	0.253
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.232
r_xyhbond_nbd_refined	0.21
r_chiral_restr	0.112
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5699
Nucleic Acid Atoms
Solvent Atoms	1239
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
CCP4	phasing