7BDZ

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (1)

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

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.964	α = 90
b = 77.964	β = 90
c = 37.291	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	1.5418

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	1.94	25.48	99	0.095	0.045	0.997	14.9	5.3		8895

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	1.94	1.97			0.44	0.249	0.808	2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	193l	1.94	25.48	8875	430	99.162	0.159	0.1562	0.2174	21.212

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]
-0.299			-0.299		0.598

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.34
r_dihedral_angle_4_deg	16.344
r_dihedral_angle_3_deg	12.039
r_dihedral_angle_1_deg	6.989
r_lrange_it	5.886
r_lrange_other	5.884
r_scangle_it	3.896
r_scangle_other	3.894
r_scbond_it	2.526
r_scbond_other	2.524
r_angle_refined_deg	2.384
r_mcangle_it	2.088
r_mcangle_other	2.085
r_mcbond_it	1.576
r_angle_other_deg	1.51
r_mcbond_other	1.443
r_nbd_other	0.309
r_symmetry_xyhbond_nbd_refined	0.255
r_xyhbond_nbd_refined	0.24
r_nbd_refined	0.224
r_symmetry_nbd_other	0.21
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_other	0.145
r_ext_dist_refined_d	0.13
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	76

Software

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