7BE0 | pdb_00007be0

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (2)

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

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.948	α = 90
b = 77.948	β = 90
c = 37.38	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 SATURN 944		2016-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5406

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	1.62	26.99	98.7	0.068	0.021	0.999	56.7	9		15018

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	1.62	1.65	86.6		0.19	0.152	0.942	3.4

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	1.62	26.99	14977	736	98.656	0.166	0.1646	0.17	0.2028	0.21	21.371

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]
-0.263			-0.263		0.525

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.508
r_dihedral_angle_4_deg	14.969
r_dihedral_angle_3_deg	11.544
r_dihedral_angle_1_deg	6.576
r_lrange_it	5.829
r_lrange_other	5.828
r_scangle_it	4.544
r_scangle_other	4.542
r_scbond_it	3.217
r_scbond_other	3.215
r_mcangle_other	2.382
r_mcangle_it	2.381
r_angle_refined_deg	1.958
r_mcbond_it	1.841
r_mcbond_other	1.665
r_angle_other_deg	1.645
r_symmetry_xyhbond_nbd_refined	0.286
r_symmetry_nbd_refined	0.282
r_nbd_other	0.277
r_xyhbond_nbd_refined	0.254
r_nbd_refined	0.225
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_other	0.164
r_ext_dist_refined_d	0.104
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.062
r_gen_planes_refined	0.02
r_bond_refined_d	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	68

Software

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