3HBD | pdb_00003hbd

Class IV chitinase structure from Picea abies at 1.8A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CNS	Homology model of the Picea abies chitinase built on barley seed chitinase (PDB entry 1CNS)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	296	20% w/v polyethylene glycol 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.004	α = 90
b = 65.579	β = 90
c = 36.481	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	100	CCD	ADSC QUANTUM 315r		2006-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9998	ESRF	ID23-1

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	1.8	50	97.4	0.078	13			14815

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)
	1.8	1.9	88.5		0.481	3.1

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	Homology model of the Picea abies chitinase built on barley seed chitinase (PDB entry 1CNS)	1.8	50	14262	750	96.69	0.17749	0.17582	0.17	0.20993	0.21	RANDOM	21.32

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]
0.32			0.35		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.286
r_dihedral_angle_3_deg	14.354
r_dihedral_angle_1_deg	4.757
r_dihedral_angle_4_deg	4.523
r_scangle_it	4.166
r_scbond_it	2.812
r_mcangle_it	1.685
r_angle_refined_deg	1.267
r_mcbond_it	0.986
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1511
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	13

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling