7BE1 | pdb_00007be1

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (3)

X-RAY DIFFRACTION

---

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	0.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.36	α = 90
b = 78.36	β = 90
c = 37.61	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		2019-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.5406	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.4	78.36	100	0.099	0.023	0.999	10.2	19.6		23665

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.47	100		2	0.519	0.701		16.6

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 (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	1.4	55.409	23665	1212	99.97	0.191	0.1901	0.2	0.2089	0.22	16.827

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]
-0.347			-0.347		0.694

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.339
r_dihedral_angle_3_deg	14.973
r_dihedral_angle_4_deg	14.543
r_lrange_it	6.85
r_lrange_other	6.653
r_dihedral_angle_1_deg	6.515
r_scangle_it	4.249
r_scangle_other	4.247
r_scbond_it	2.801
r_scbond_other	2.798
r_mcangle_other	2.168
r_mcangle_it	2.162
r_angle_refined_deg	1.866
r_angle_other_deg	1.644
r_mcbond_it	1.556
r_mcbond_other	1.466
r_nbd_other	0.27
r_nbd_refined	0.252
r_ext_dist_refined_d	0.24
r_xyhbond_nbd_refined	0.239
r_symmetry_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.158
r_chiral_restr	0.102
r_metal_ion_refined	0.097
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.074
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.008
r_xyhbond_nbd_other	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	88

Software

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