8RVX | pdb_00008rvx

Cph1 phytochrome PAS-GAF-PHY Y176H mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VEA	Only the residues 4-313
experimental model	PDB	2VEA	Only the residues 331-443, and 488-514

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	0.3 M ammonium formate 0.1 M HEPES pH 6.9 18% (w/v) Sokalan CP7

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.873	α = 90
b = 135.873	β = 90
c = 355.644	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	100	PIXEL	DECTRIS PILATUS3 6M		2020-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.696	47.651	99.3	0.8	0.157	0.982	6.3	25.8		36339

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.696	3.791	97.2		3.702	0.743	0.398	1.2	24.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.696	47.651	36303	1760	99.078	0.268	0.2657	0.2644	0.3068	0.3029	114.078

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]
-0.487			-0.487		0.975

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.402
r_dihedral_angle_6_deg	15.312
r_lrange_it	6.601
r_lrange_other	6.601
r_dihedral_angle_1_deg	6.37
r_dihedral_angle_2_deg	5.899
r_mcangle_it	3.354
r_mcangle_other	3.354
r_scangle_it	2.354
r_scangle_other	2.354
r_mcbond_it	1.881
r_mcbond_other	1.881
r_angle_refined_deg	1.338
r_chiral_restr_other	1.222
r_scbond_it	1.204
r_scbond_other	1.204
r_angle_other_deg	0.844
r_symmetry_xyhbond_nbd_refined	0.443
r_symmetry_nbd_refined	0.368
r_nbd_other	0.32
r_symmetry_nbd_other	0.224
r_nbd_refined	0.22
r_ncsr_local_group_5	0.186
r_nbtor_refined	0.18
r_ncsr_local_group_1	0.18
r_ncsr_local_group_3	0.179
r_ncsr_local_group_4	0.174
r_ncsr_local_group_6	0.174
r_ncsr_local_group_2	0.164
r_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_other	0.123
r_symmetry_xyhbond_nbd_other	0.109
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_ext_dist_refined_b	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15506
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	172

Software

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