9RBV | pdb_00009rbv

X-ray structure of lysozyme when is treated with Cs2[V(V)2O4(mal)2]2H2O at 310K

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	310	1.1 M sodium chloride and 0.1 M sodium acetate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 37.4	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	310	PIXEL	DECTRIS PILATUS 6M		2024-11-20	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)	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	2.09	55.93	95.7	0.997	8.2	7.6		53940

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.13			0.323

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.09	55.93	7102	302	81.023	0.218	0.2133	0.2176	0.2935	0.292	38.357

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]
-0.509			-0.509		1.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.332
r_dihedral_angle_4_deg	23.459
r_dihedral_angle_3_deg	16.28
r_dihedral_angle_1_deg	7.87
r_lrange_it	7.69
r_lrange_other	7.681
r_scangle_it	6.095
r_scangle_other	6.078
r_mcangle_it	4.147
r_mcangle_other	4.147
r_scbond_it	4.059
r_scbond_other	4.051
r_mcbond_it	3.065
r_mcbond_other	3.038
r_angle_refined_deg	1.569
r_angle_other_deg	1.325
r_xyhbond_nbd_refined	0.266
r_nbd_refined	0.228
r_symmetry_nbd_other	0.196
r_nbd_other	0.181
r_symmetry_nbd_refined	0.171
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.131
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.061
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	4

Software

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