2QX3 | pdb_00002qx3

Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	0.1M Hepes, 25% polyethylene glycol 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.183	α = 71.72
b = 53.158	β = 80.03
c = 73.057	γ = 69.1

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS HTC		2007-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	25	83.6	0.058	20.1	1.9	35612	35612

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)
	2	2.07	37.2		0.21		1.7	1584

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 1AIR	2	25	35612	1785	83.29	0.16	0.157	0.1689	0.211	0.2195	RANDOM	23.302

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]
-0.36	0.46	0.08	-0.19	-0.38	0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.417
r_dihedral_angle_4_deg	16.082
r_dihedral_angle_3_deg	13.588
r_dihedral_angle_1_deg	6.609
r_scangle_it	1.818
r_scbond_it	1.195
r_angle_refined_deg	1.182
r_mcangle_it	0.717
r_mcbond_it	0.411
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5181
Nucleic Acid Atoms
Solvent Atoms	598
Heterogen Atoms	25

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction