4HPI | pdb_00004hpi

Crystal Structure of Hen Egg White Lysozyme complex with GN2-M

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BWJ	PDB ENTRY 1BWJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS(pH6.5), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.416	α = 90
b = 77.416	β = 90
c = 38.042	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	95	CCD	ADSC QUANTUM 315r		2012-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.19	54.74	99.8	0.074	76	13.8		37127

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.19	1.21	99.4		0.262	10.3	12	21972

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	PDB ENTRY 1BWJ	1.19	50	35699	1877	99.86	0.16823	0.16759	0.1676	0.18037	0.1816	RANDOM	13.497

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]
-0.12			-0.12		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.383
r_dihedral_angle_4_deg	14.799
r_dihedral_angle_3_deg	12.379
r_dihedral_angle_1_deg	5.637
r_sphericity_free	3.283
r_sphericity_bonded	3.154
r_scangle_it	2.576
r_scbond_it	1.711
r_mcangle_it	1.392
r_angle_refined_deg	1.211
r_rigid_bond_restr	0.894
r_mcbond_it	0.82
r_chiral_restr	0.093
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	992
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	39

Software

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