8DZ7 | pdb_00008dz7

Hen lysozyme in orthorhombic 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	1WTM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	318	Reservoir contained 1.0-1.1 M NaCl, 0.1 M NaOAc pH 4.6. Drops of 30 microliters contained a 1:2 ratio of 90-100 mg/mL protein and reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.486	α = 90
b = 56.401	β = 90
c = 73.852	γ = 90

Symmetry
Space Group	P 21 21 21

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	2016-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.976	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	1.34	44.82	96.9	0.039	0.041	0.011	0.999	36	12.1		28707

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	1.34	1.36	68.4		0.238	0.295	0.17	0.898	3.8	2.2

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	1wtm	1.34	44.82	28632	1417	96.756	0.119	0.1179	0.12	0.1362	0.14	23.948

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]
-0.002			0.356		-0.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.963
r_rigid_bond_restr	22.399
r_dihedral_angle_4_deg	22.277
r_scbond_it	13.036
r_scbond_other	13.007
r_dihedral_angle_3_deg	12.276
r_scangle_it	12.24
r_scangle_other	12.201
r_lrange_other	8.033
r_lrange_it	8.029
r_dihedral_angle_1_deg	5.991
r_mcangle_other	5.908
r_mcangle_it	5.89
r_mcbond_it	5.008
r_mcbond_other	4.971
r_angle_refined_deg	2.096
r_angle_other_deg	2.025
r_metal_ion_refined	0.467
r_symmetry_nbd_refined	0.284
r_nbd_refined	0.266
r_nbd_other	0.208
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.183
r_chiral_restr	0.157
r_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_refined	0.041
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	2

Software

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