3IJU | pdb_00003iju

Chicken egg white lysozyme by highly ordered APA (Anodic Porous Alumina) nanotemplate crystallization method

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	293	0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.064	α = 90
b = 79.064	β = 90
c = 37.544	γ = 90

Symmetry
Space Group	P 43 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	mirror	2006-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.9465	ESRF	ID13

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	1.6	55.907	98.9	0.099	0.099	21.6	11		16036

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)
	1.6	1.69	100		0.221	0.221	2.8	11.5	2322

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 2yvb	1.6	21.57	16005	803	98.55	0.226	0.225	0.2223	0.237	0.2325	RANDOM	18.645

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]
0.24			0.24		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.75
r_dihedral_angle_4_deg	19.44
r_dihedral_angle_3_deg	14.671
r_dihedral_angle_1_deg	5.58
r_scangle_it	2.474
r_mcangle_it	2.155
r_scbond_it	1.576
r_mcbond_it	1.32
r_angle_refined_deg	1.252
r_symmetry_vdw_refined	0.325
r_nbtor_refined	0.309
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing