4NY5

X-ray structure of the adduct formed between hen egg white lysozyme and NAMI-A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	Crystals of the HEWL/NAMI-A adduct suitable for X-ray diffraction studies Have been grown by hanging drop vapor diffusion by mixing 1 L of 20 mg/mL HEWL/NAMI-A complex (protein to metal ratio 1:10) with an equal volume of reservoir solution containing 1.0 M NaCl and 50 mM sodium acetate pH 4.5. These crystals were fished with nylon loops and flash-frozen at 100 K using nitrogen gas, without cryoprotectant. This procedure partly dehydrates the crystals, enhancing in some cases the resolution of X-ray diffraction data, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.772	α = 90
b = 77.772	β = 90
c = 37.316	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+	mirrors	2013-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	22.15	98.9	0.095	5.3	5.3	10143	10143

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 4J1A	1.85	22.15	9628	490	98.91	0.17933	0.17626	0.23994	RANDOM	26.913

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]
-0.2			-0.2		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.814
r_dihedral_angle_3_deg	14.422
r_dihedral_angle_4_deg	14.15
r_long_range_B_refined	7.92
r_long_range_B_other	7.77
r_dihedral_angle_1_deg	5.974
r_scangle_other	5.475
r_scbond_it	3.63
r_scbond_other	3.628
r_mcangle_it	2.912
r_mcangle_other	2.911
r_mcbond_it	2.244
r_mcbond_other	2.227
r_angle_refined_deg	1.768
r_angle_other_deg	0.961
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing