4NGY | pdb_00004ngy

Dialyzed HEW lysozyme batch crystallized in 0.75 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, 0.75 M YbCl3, pH 4.5, EVAPORATION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.666	α = 90
b = 78.666	β = 90
c = 37.151	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	1.35	35.18	99.1	0.061	12.8	4.2		48465			16.1

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	1.35	1.43	98.5		0.326	2.9	3.8

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	1.35	55.63	46490	23404	2524	99.02	0.19304	0.19061	0.21	0.21586	0.24	RANDOM	21.322

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]
0.72			0.72		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.316
r_dihedral_angle_3_deg	15.118
r_dihedral_angle_4_deg	14.66
r_dihedral_angle_1_deg	5.985
r_scbond_it	3.907
r_mcangle_it	2.343
r_mcbond_it	1.755
r_angle_refined_deg	1.697
r_mcbond_other	1.668
r_angle_other_deg	0.954
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	145
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