2IGB | pdb_00002igb

Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, UMP-bound form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1M sodium citrate, 0.2M sodium chloride, 1.0M diammonium hydrogen phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.281	α = 90
b = 96.752	β = 90
c = 63.104	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2006-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97000	APS	23-ID-B

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	1.68	50		0.079	0.057		7		46630			21.5

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)
	1.68	1.74			0.93	0.62		5.5

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 (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 1NON	1.68	41.31	44224	2356	99.28	0.18452	0.18249	0.18	0.22375	0.22	RANDOM	23.579

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]
1.45			-0.57		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.593
r_dihedral_angle_4_deg	21.493
r_dihedral_angle_3_deg	16.38
r_dihedral_angle_1_deg	6.131
r_scangle_it	4.187
r_scbond_it	2.661
r_mcangle_it	1.846
r_angle_refined_deg	1.702
r_mcbond_it	1.198
r_symmetry_hbond_refined	0.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.593
r_dihedral_angle_4_deg	21.493
r_dihedral_angle_3_deg	16.38
r_dihedral_angle_1_deg	6.131
r_scangle_it	4.187
r_scbond_it	2.661
r_mcangle_it	1.846
r_angle_refined_deg	1.702
r_mcbond_it	1.198
r_symmetry_hbond_refined	0.356
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.139
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2843
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.