3ZSC | pdb_00003zsc

Catalytic function and substrate recognition of the pectate lyase from Thermotoga maritima

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.2		pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.602	α = 90
b = 80.602	β = 90
c = 148.819	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH SX-165			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	1.95	14	100	0.1	18.6	5.6		26478		2

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	1.95	14	100		0.44	3.5

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 2BSP	1.94	63.25	25137	1339	99.62	0.18168	0.17877	0.18	0.23699	0.23	RANDOM	33.708

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]
0.9	0.45		0.9		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.455
r_dihedral_angle_4_deg	16.404
r_dihedral_angle_3_deg	14.75
r_dihedral_angle_1_deg	6.893
r_scangle_it	3.619
r_scbond_it	2.458
r_angle_refined_deg	1.699
r_mcangle_it	1.67
r_mcbond_it	1.019
r_nbtor_refined	0.326
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.132
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2568
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
EPMR	phasing