5EBH | pdb_00005ebh

Crystal Structure HEW Lysozyme processed with the CrystalDirect automated mounting and cryo-cooling technology

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour diffusion method and CrystalDirect plates . Crystallization experiments were set up with 100 nl of sample and 100 nl of crystallization solution on the inner surface of the films within a CrystalDirect plate with a Cartesian PixSys robot (Cartesian Technologies). The crystallization solution was 0.1 M sodium acetate, pH=4.6 and 1.25 M sodium chloride.

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.801	α = 90
b = 78.801	β = 90
c = 37.267	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		2015-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

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	1.2	19.7	100	0.06	17.2	8.4		37274

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4b0d	1.2	19.7	35325	1896	99.92	0.17452	0.17308	0.18	0.20102	0.21	RANDOM	13.983

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]
0.26			0.26		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.364
r_sphericity_free	17.92
r_dihedral_angle_1_deg	15.912
r_dihedral_angle_3_deg	11.675
r_dihedral_angle_4_deg	9.846
r_sphericity_bonded	4.068
r_rigid_bond_restr	4.035
r_angle_other_deg	2.18
r_long_range_B_refined	2.062
r_angle_refined_deg	1.9
r_long_range_B_other	1.361
r_mcangle_other	0.766
r_mcangle_it	0.718
r_scangle_other	0.712
r_mcbond_it	0.66
r_scbond_it	0.644
r_scbond_other	0.568
r_mcbond_other	0.519
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	977
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing