4B1A | pdb_00004b1a

Crystal structure of lysozyme with Keggin molecule

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		2-10% (M/V) NACL AND 0.1 M ACETATE BUFFER PH 4.5 (THE PROTEIN:WELL SOLUTION RATIO IN THE DROP WAS 1:1 WITH THE FINAL DROP VOLUME OF 4 MICROLITER USING A PROTEIN STOCK CONCENTRATION OF AROUND 50 MG/ML.

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.96	α = 90
b = 77.96	β = 90
c = 36.41	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	160	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.67	30.38	99.6	0.02	29.7	13.5		13544		-1

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	1.67	1.76	100		0.1	6.4	13.4

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 193L	1.67	30.38	12793	667	99.48	0.21501	0.21249	0.22	0.26664	0.27	RANDOM	22.674

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]
-1.47			-1.47		2.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.837
r_dihedral_angle_4_deg	20.704
r_dihedral_angle_3_deg	14.229
r_dihedral_angle_1_deg	7.299
r_scangle_it	4.522
r_scbond_it	2.999
r_mcangle_it	1.891
r_angle_refined_deg	1.84
r_mcbond_it	1.194
r_angle_other_deg	1.184
r_mcbond_other	0.375
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	987
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing