7XND | pdb_00007xnd

Crystal structure of Phosphomevalonate kinase from Silkworm

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	289	1.8 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.27	40.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.07	α = 90
b = 54.07	β = 90
c = 123.12	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 PILATUS 6M		2019-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (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	1.6	32.48	99.9	0.066	0.068	27.1	23.2		24974

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	99.9		1.236	0.32		15.6

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	3CH4	1.6	32.48	24902	1264	99.872	0.212	0.2097	0.22	0.2468	0.25	32.694

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]
-0.46			-0.46		0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.964
r_dihedral_angle_4_deg	15.851
r_dihedral_angle_3_deg	12.837
r_lrange_other	8.241
r_lrange_it	8.239
r_scangle_it	7.221
r_scangle_other	7.218
r_dihedral_angle_1_deg	6.627
r_scbond_it	4.798
r_scbond_other	4.795
r_mcangle_it	3.836
r_mcangle_other	3.834
r_mcbond_it	2.965
r_mcbond_other	2.964
r_angle_other_deg	2.259
r_angle_refined_deg	1.645
r_nbd_other	0.298
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.216
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.072
r_bond_other_d	0.034
r_gen_planes_other	0.015
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1389
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing