8BD0 | pdb_00008bd0

Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein modification

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G98	2G98

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.8	298	50 mM phosphate buffer pH 7.8, 20 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.9	α = 90
b = 83.7	β = 90
c = 101	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 EIGER X 1M		2019-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	25600		25600

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	101.13	99.99	0.9956	0.2717	2.71	50.3		31629

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	100		0.14	1.94	0.6	34.7

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	2G98	2	101	25054	1718	84.79	0.20727	0.20437	0.21	0.24971	0.25	RANDOM	35.637

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]
-0.43			0.26		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.078
r_dihedral_angle_4_deg	19.74
r_dihedral_angle_3_deg	16.778
r_long_range_B_other	9.318
r_long_range_B_refined	9.317
r_dihedral_angle_1_deg	7.207
r_scangle_other	6.041
r_scbond_it	3.887
r_scbond_other	3.886
r_mcangle_other	3.447
r_mcangle_it	3.446
r_mcbond_it	2.311
r_mcbond_other	2.305
r_angle_refined_deg	1.492
r_angle_other_deg	1.238
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2858
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing