4XN6 | pdb_00004xn6

Crystal structure at room temperature of hen-egg lysozyme in complex with benzamidine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	NaOAc 100mM ,4% (w/v) NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.292	α = 90
b = 79.292	β = 90
c = 38.073	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	298	CCD	ADSC QUANTUM 315r		2014-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9797	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	38.1	99.5	2.5	4.3		21988

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.35	38.1	21988	1285	94.95	0.1397	0.1383	0.15	0.1655	0.17	RANDOM	17.371

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]
-0.13			-0.13		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.08
r_sphericity_free	20.807
r_dihedral_angle_4_deg	19.505
r_dihedral_angle_3_deg	12.874
r_sphericity_bonded	5.91
r_dihedral_angle_1_deg	5.682
r_rigid_bond_restr	1.918
r_mcangle_it	1.673
r_mcbond_it	1.306
r_mcbond_other	1.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.08
r_sphericity_free	20.807
r_dihedral_angle_4_deg	19.505
r_dihedral_angle_3_deg	12.874
r_sphericity_bonded	5.91
r_dihedral_angle_1_deg	5.682
r_rigid_bond_restr	1.918
r_mcangle_it	1.673
r_mcbond_it	1.306
r_mcbond_other	1.301
r_angle_refined_deg	1.239
r_angle_other_deg	0.857
r_chiral_restr	0.084
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	9

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.