3SIM | pdb_00003sim

Crystallographic structure analysis of family 18 Chitinase from Crocus vernus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	0.1M CHES, 20 % (w/v) PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 172.27	α = 90
b = 37.08	β = 127.01
c = 126.37	γ = 90

Symmetry
Space Group	C 1 2 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	MAR CCD 165 mm		2010-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

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	2.1	30	96.3	0.012	0.012	2.2	3.5	37995	34613	2.5	1

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	2.1	2.2	95.7		0.43	0.43	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1NAR	2.1	30	37995	34613	1831	95.97	0.15838	0.15537	0.21347	0.2106	RANDOM	15.881

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]
-0.17		-0.65	-0.29		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.33
r_dihedral_angle_4_deg	20.86
r_dihedral_angle_3_deg	13.901
r_dihedral_angle_1_deg	5.728
r_scangle_it	3.709
r_scbond_it	2.627
r_angle_refined_deg	1.628
r_mcangle_it	1.626
r_mcbond_it	0.946
r_chiral_restr	0.126
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4288
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	16

Software

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