8BPI | pdb_00008bpi

Human Gamma-D crystallin R36S mutant after UV illumination

X-RAY DIFFRACTION

---

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
2.32	47

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 16M		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	100	0.9546	0.2277	3.19	70.2		31633

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		0.2283	1.669	0.68	48.3

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	2G98	2	101	27049	1746	85.666	0.2	0.1973	0.2	0.2407	0.25	37.112

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]
-0.682			0.323		0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.712
r_dihedral_angle_4_deg	19.903
r_dihedral_angle_3_deg	16.439
r_lrange_it	9.474
r_lrange_other	9.473
r_dihedral_angle_1_deg	6.834
r_scangle_it	6.381
r_scangle_other	6.38
r_scbond_it	3.92
r_scbond_other	3.919
r_mcangle_it	3.848
r_mcangle_other	3.848
r_mcbond_it	2.555
r_mcbond_other	2.541
r_angle_refined_deg	1.446
r_angle_other_deg	1.24
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.186
r_nbd_other	0.179
r_nbd_refined	0.174
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.098
r_ncsr_local_group_1	0.086
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2871
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

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