4N5R | pdb_00004n5r

Hen egg-white lysozyme phased using free-electron laser data

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	3	293	20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0, stored in 8% NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in storage solution + 100 mM gadoteridol, batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 39.2	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	293	PIXEL	Cornell-SLAC Pixel Array Detector (CSPAD)		2013-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.45	SLAC LCLS	CXI

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	2.1	40	100				7294

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 1VDS	2.1	39.55	7287	7294	385	99.99	0.2322	0.23098	0.22	0.25632	0.25	RANDOM	32.54

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]
-0.27			-0.27		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.663
r_dihedral_angle_4_deg	18.229
r_dihedral_angle_3_deg	14.043
r_dihedral_angle_1_deg	5.711
r_scangle_it	2.224
r_scbond_it	1.347
r_angle_refined_deg	1.285
r_mcangle_it	0.862
r_angle_other_deg	0.841
r_mcbond_it	0.435
r_mcbond_other	0.08
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	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_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	992
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	58

Software

Software
Software Name	Purpose
DAQ	data collection
PHASER	phasing
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling