2HU3 | pdb_00002hu3

Parent Structure of Hen Egg White Lysozyme grown in acidic pH 4.8. Refinement for comparison with crosslinked molecules of lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	0.1M Na Acetate, pH 4.8, 7% NaCl, 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.87	α = 90
b = 78.87	β = 90
c = 36.788	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	ADSC QUANTUM 210	mirrors	2005-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9737	ESRF	ID29

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	1.3	55.73	100	0.057	0.057	10.5	27	29161	29161		-3	10.43

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	1.3	1.32	100		0.538	0.52	3.92	15.9	1416

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	FOURIER SYNTHESIS	THROUGHOUT	In-house model	1.3	55.73	-3	29111	29111	1477	99.98	0.105	0.105	0.103	0.11	0.145	0.14	RANDOM	10.981

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]
0.09			0.09		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.179
r_dihedral_angle_4_deg	19.117
r_sphericity_free	17.031
r_dihedral_angle_3_deg	11.707
r_scangle_it	8.325
r_sphericity_bonded	7.057
r_scbond_it	6.984
r_dihedral_angle_1_deg	5.873
r_mcangle_it	4.52
r_mcbond_it	3.603
r_rigid_bond_restr	3.475
r_mcbond_other	2.723
r_angle_refined_deg	1.571
r_angle_other_deg	1.141
r_symmetry_vdw_other	0.363
r_nbd_refined	0.268
r_symmetry_vdw_refined	0.256
r_nbd_other	0.23
r_xyhbond_nbd_refined	0.214
r_metal_ion_refined	0.206
r_symmetry_hbond_refined	0.189
r_nbtor_refined	0.186
r_chiral_restr	0.122
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing