8DYZ | pdb_00008dyz

Hen lysozyme in tetragonal space group at ambient temperature - diffuse scattering dataset

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	295	Reservoir contained 1.1 M NaCl, 0.1 M NaOAc pH 4.8. Drops contained 2 microliters each of 40 mg/mL protein and well solution.

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.632	α = 90
b = 79.632	β = 90
c = 38.296	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	PIXEL	DECTRIS PILATUS3 6M	100 micron collimator	2017-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9768	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.27	39.82	98	0.046	0.047	0.009	1	39.2	23.8		32284

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.27	1.29	78.1		0.38	0.426	0.184	0.878	3.7	4.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	193L	1.272	39.82	32215	1659	97.885	0.116	0.1149	0.12	0.1332	0.13	25.565

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]
0.198			0.198		-0.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.277
r_rigid_bond_restr	30.472
r_scbond_it	29.262
r_scbond_other	29.235
r_dihedral_angle_4_deg	26.665
r_scangle_it	21.924
r_scangle_other	21.911
r_lrange_other	18.149
r_lrange_it	18.109
r_mcbond_it	16.227
r_mcbond_other	16.181
r_dihedral_angle_3_deg	11.14
r_mcangle_other	11.017
r_mcangle_it	11.016
r_dihedral_angle_1_deg	6.014
r_angle_refined_deg	2.054
r_angle_other_deg	1.599
r_nbd_refined	0.23
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.169
r_nbd_other	0.159
r_chiral_restr	0.131
r_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.058
r_symmetry_xyhbond_nbd_refined	0.033
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.008
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Coot	model building
XDS	data reduction
REFMAC	phasing