8AJ4 | pdb_00008aj4

X-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (Structure A')

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	7.5	293	2.0 M sodium formate 0.1 M hepes pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.08	α = 90
b = 77.08	β = 90
c = 38.09	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	PIXEL	DECTRIS PILATUS 6M		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.22	38.54	99.7	0.09	0.999	19.1	18.6		34981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.22	1.24	97.3		1.005	0.747	3.1	12.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	193L	1.22	38.54	34951	1728	99.695	0.179	0.1777	0.19	0.2026	0.2	17.152

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.437
r_dihedral_angle_4_deg	22.202
r_dihedral_angle_3_deg	13.275
r_dihedral_angle_1_deg	6.17
r_lrange_other	5.701
r_lrange_it	5.532
r_scangle_other	3.789
r_scangle_it	3.642
r_scbond_other	2.413
r_scbond_it	2.344
r_mcangle_other	2.251
r_mcangle_it	2.239
r_angle_refined_deg	1.813
r_angle_other_deg	1.603
r_mcbond_it	1.505
r_mcbond_other	1.469
r_nbd_refined	0.24
r_symmetry_nbd_other	0.194
r_nbd_other	0.186
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_nbd_refined	0.148
r_metal_ion_refined	0.123
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.019
r_gen_planes_refined	0.016
r_ext_dist_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing