3KRG | pdb_00003krg

Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O0V	PDB entry 2O0V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, 50% PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.626	α = 90
b = 69.066	β = 113.85
c = 59.656	γ = 90

Symmetry
Space Group	P 1 21 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 225 mm CCD	mirrors	2007-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.970	SRS	PX10.1

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	1.9	69.01	97.2	0.057	0.067	23.8	3.7		28827			8.608

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)
	1.9	2	96.1		0.067	0.067	18.3	3.7	4138

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2O0V	1.9	29.18	27344	1459	96.88	0.135	0.132	0.13	0.196	0.19	RANDOM	8.969

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.383
r_dihedral_angle_3_deg	12.384
r_dihedral_angle_4_deg	11.667
r_dihedral_angle_1_deg	6.498
r_scangle_it	3.646
r_scbond_it	2.676
r_angle_refined_deg	1.648
r_mcangle_it	1.444
r_mcbond_it	0.787
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.383
r_dihedral_angle_3_deg	12.384
r_dihedral_angle_4_deg	11.667
r_dihedral_angle_1_deg	6.498
r_scangle_it	3.646
r_scbond_it	2.676
r_angle_refined_deg	1.648
r_mcangle_it	1.444
r_mcbond_it	0.787
r_chiral_restr	0.135
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3055
Nucleic Acid Atoms
Solvent Atoms	723
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.