3AW6 | pdb_00003aw6

Crystal structure of tetragonal hen egg white lysozyme at 84.2% relative humidity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JIS	PDB ENTRY 1JIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	3-8%(w/v) NaCl, 100mM Na acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.484	α = 90
b = 79.484	β = 90
c = 37.886	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	300	IMAGE PLATE	RIGAKU RAXIS IV		2009-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

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	2.1	50	95.9	0.048	12.5	3.4	7214	7214

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	2.1	2.18	96.6		0.085	10.5

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 1JIS	2.1	19.06	6866	6866	325	96.34	0.15783	0.15783	0.15493	0.1588	0.21994	0.2119	RANDOM	20.452

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.78
r_dihedral_angle_4_deg	23.946
r_dihedral_angle_3_deg	15.607
r_dihedral_angle_1_deg	6.167
r_scangle_it	5.001
r_scbond_it	3.088
r_mcangle_it	1.869
r_angle_refined_deg	1.477
r_mcbond_it	0.972
r_nbtor_refined	0.298
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.121
r_chiral_restr	0.11
r_symmetry_hbond_refined	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	7

Software

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