3CB7 | pdb_00003cb7

The crystallographic structure of the digestive lysozyme 2 from Musca domestica at 1.9 Ang.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	291	The 3 uL drop was formed by 1.5 uL of protein solution at 9.8 mg/mL in 10 mM MES pH 5.5 plus 1.3 uL of 28% 2-propanol, 0.115 M sodium citrate pH 4.2 and 21% PEG 4000 plus 0.2 uL of 0.2 M ammonium acetate, 0.1 M sodium citrate pH 5.6 and 30% MPD., VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.903	α = 90
b = 96.4	β = 90
c = 33.27	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	MAR CCD 165 mm	mirrors	2006-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1

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	1.9	30	90.7	0.089	14.4	3.9	17698	17698			23.3

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	1.9	1.97	74.1		0.304	2.1	1.8	1423

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 (All)	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 2fbd	1.9	30	17674	17674	910	95.9	0.18732	0.18732	0.18355	0.19	0.25789	0.26	RANDOM	40.144

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]
-1.67			-3.92		5.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.259
r_dihedral_angle_4_deg	17.912
r_dihedral_angle_3_deg	15.428
r_dihedral_angle_1_deg	7.553
r_scangle_it	2.745
r_scbond_it	1.949
r_angle_refined_deg	1.664
r_mcangle_it	1.071
r_mcbond_it	0.668
r_nbtor_refined	0.321
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.193
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.105
r_bond_refined_d	0.017
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2006
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing