4NGW | pdb_00004ngw

Dialyzed HEW lysozyme batch crystallized in 0.5 M YbCl3 and collected at 100 K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L	PDB ENTRY 193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	293	Dialyzed lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, EVAPORATION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.665	α = 90
b = 78.665	β = 90
c = 37.129	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	MIRRORS	2013-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.37	99.4935	99	0.051	14.1	3.4		46325			15.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.45	97.4		0.294	3.48	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 193L	1.37	55.62	44465	22474	2409	99.24	0.16495	0.1625	0.18	0.18766	0.2	RANDOM	19.299

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]
-0.07			-0.07		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.629
r_dihedral_angle_2_deg	35.036
r_dihedral_angle_4_deg	17.658
r_dihedral_angle_3_deg	13.519
r_sphericity_bonded	9.297
r_dihedral_angle_1_deg	5.5
r_rigid_bond_restr	2.219
r_scbond_it	1.956
r_mcangle_it	1.801
r_mcbond_it	1.41
r_angle_refined_deg	1.31
r_mcbond_other	1.268
r_angle_other_deg	0.854
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling
TRUNCATE	data scaling
MxCuBE	data collection