5YKY | pdb_00005yky

Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 mM Rose Bengal and 10mM H2PtCl6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	0.7M NaCl, 0.1 M acetate buffer

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.458	α = 90
b = 78.458	β = 90
c = 36.647	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	RIGAKU JUPITER 210		2017-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.88	55.48	99.48	18.7	13.1		9257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.92	99.86		24.28	9.6

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	193L	1.88	55.48	9257	480	99.48	0.18454	0.18157	0.19	0.23748	0.25	RANDOM	33.867

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	38.225
r_dihedral_angle_4_deg	24.271
r_dihedral_angle_3_deg	15.217
r_long_range_B_other	7.891
r_long_range_B_refined	7.884
r_dihedral_angle_1_deg	6.94
r_scangle_other	6.564
r_scbond_it	4.338
r_scbond_other	4.332
r_mcangle_other	3.684
r_mcangle_it	3.681
r_mcbond_it	2.885
r_mcbond_other	2.875
r_angle_refined_deg	1.815
r_angle_other_deg	1.166
r_chiral_restr	0.126
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	15

Software

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